1
|
Zuo D, Lei S, Qian F, Gu L, Wang H, Du X, Zeng T, Zhu B. Genome-wide identification and stress response analysis of BcaCPK gene family in amphidiploid Brassica carinata. BMC Plant Biol 2024; 24:296. [PMID: 38632529 PMCID: PMC11022436 DOI: 10.1186/s12870-024-05004-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Calcium-dependent protein kinases (CPKs) are crucial for recognizing and transmitting Ca2+ signals in plant cells, playing a vital role in growth, development, and stress response. This study aimed to identify and detect the potential roles of the CPK gene family in the amphidiploid Brassica carinata (BBCC, 2n = 34) using bioinformatics methods. RESULTS Based on the published genomic information of B. carinata, a total of 123 CPK genes were identified, comprising 70 CPK genes on the B subgenome and 53 on the C subgenome. To further investigate the homologous evolutionary relationship between B. carinata and other plants, the phylogenetic tree was constructed using CPKs in B. carinata and Arabidopsis thaliana. The phylogenetic analysis classified 123 family members into four subfamilies, where gene members within the same subfamily exhibited similar conserved motifs. Each BcaCPK member possesses a core protein kinase domain and four EF-hand domains. Most of the BcaCPK genes contain 5 to 8 introns, and these 123 BcaCPK genes are unevenly distributed across 17 chromosomes. Among these BcaCPK genes, 120 replicated gene pairs were found, whereas only 8 genes were tandem duplication, suggesting that dispersed duplication mainly drove the family amplification. The results of the Ka/Ks analysis indicated that the CPK gene family of B. carinata was primarily underwent purification selection in evolutionary selection. The promoter region of most BcaCPK genes contained various stress-related cis-acting elements. qRT-PCR analysis of 12 selected CPK genes conducted under cadmium and salt stress at various points revealed distinct expression patterns among different family members in response to different stresses. Specifically, the expression levels of BcaCPK2.B01a, BcaCPK16.B02b, and BcaCPK26.B02 were down-regulated under both stresses, whereas the expression levels of other members were significantly up-regulated under at least one stress. CONCLUSION This study systematically identified the BcaCPK gene family in B. carinata, which contributes to a better understanding the CPK genes in this species. The findings also serve as a reference for analyzing stress responses, particularly in relation to cadmium and salt stress in B. carinata.
Collapse
Affiliation(s)
- Dan Zuo
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Shaolin Lei
- Guizhou Institute of Oil Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550009, China
| | - Fang Qian
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Lei Gu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Hongcheng Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Tuo Zeng
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China.
| | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China.
| |
Collapse
|
2
|
Biswas P, Kumari A, Modi A, Kumar N. Improvement and regulation of steviol glycoside biosynthesis in Stevia rebaudiana Bertoni. Gene 2024; 891:147809. [PMID: 37722610 DOI: 10.1016/j.gene.2023.147809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/20/2023]
Abstract
Stevia rebaudiana Bertoni is a natural sweetener plant that is progressively used not only for its sweetening properties but also for its medicinal properties. The plant contains steviol glycoside (SG) which is reported to be up to 300 times sweeter than sucrose. The plant is said to have no side effects on human health and has been approved by FDA. On the basis of previous studies and available databases, this review discusses the extensive understanding of the different approaches for enhancements of SG in S. rebaudiana. To improve the SG biosynthesis, application of different stress, elicitors, induction of polyploidy, cell culture, genetic engineering, and transcriptomic approaches have been addressed. A brief discussion about the cloning and characterization of important genes of the metabolic pathway of SG biosynthesis is also discussed along with various metabolic engineering pathways viz. methylerythritol 4- phosphate (MEP) and mevalonate (MVA) pathways. This review paper also discusses the different aspects as well as the effects of various nanoparticles on S. rebaudiana growth and development, as well as SG biosynthesis.
Collapse
Affiliation(s)
- Pritom Biswas
- Department of Biotechnology, Central University of South Bihar, Gaya 824236, Bihar, India
| | - Ankita Kumari
- Department of Biotechnology, Central University of South Bihar, Gaya 824236, Bihar, India
| | - Arpan Modi
- Institute of Plant Science, Volcani Center, ARO, Rishon LeZion, Israel
| | - Nitish Kumar
- Department of Biotechnology, Central University of South Bihar, Gaya 824236, Bihar, India.
| |
Collapse
|
3
|
Salimi Z, Rostami M, Milasi YE, Mafi A, Raoufinia R, Kiani A, Sakhaei F, Ghezelbash B, Butler AE, Mohammad-Sadeghipour M, Sahebkar A. Unfolded Protein Response Signaling in Hepatic Stem Cell Activation in Liver Fibrosis. Curr Protein Pept Sci 2024; 25:59-70. [PMID: 37608655 DOI: 10.2174/1389203724666230822085951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/10/2023] [Accepted: 07/06/2023] [Indexed: 08/24/2023]
Abstract
Frequent exposure to various external and internal adverse forces (stresses) disrupts cell protein homeostasis through endoplasmic reticulum (ER) capacity saturation. This process leads to the unfolded protein response (UPR), which aims to re-establish/maintain optimal cellular equilibrium. This complex mechanism is involved in the pathogenesis of various disorders, such as metabolic syndrome, fibrotic diseases, neurodegeneration, and cancer, by altering cellular metabolic changes integral to activating the hepatic stellate cells (HSCs). The development of hepatic fibrosis is one of the consequences of UPR activation. Therefore, novel therapies that target the UPR pathway effectively and specifically are being studied. This article covers the involvement of the UPR signaling pathway in cellular damage in liver fibrosis. Investigating the pathogenic pathways related to the ER/UPR stress axis that contribute to liver fibrosis can help to guide future drug therapy approaches.
Collapse
Affiliation(s)
- Zohreh Salimi
- Department of Clinical Biochemistry, School of Pharmacy & Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mehdi Rostami
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Yaser Eshaghi Milasi
- Department of Clinical Biochemistry, School of Pharmacy & Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Alireza Mafi
- Department of Clinical Biochemistry, School of Pharmacy & Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
- Nutrition and Food Security Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ramin Raoufinia
- Medical Genetics and Molecular Medicine Department, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Amirhossein Kiani
- Department of Immunology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Fariba Sakhaei
- Department of Clinical Biochemistry, School of Pharmacy & Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Behrooz Ghezelbash
- Department of Immunology, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Alexandra E Butler
- Research Department, Royal College of Surgeons in Ireland, Bahrain, PO Box 15503, Adliya, Bahrain
| | - Maryam Mohammad-Sadeghipour
- Department of Clinical Biochemistry, Afzalipoor Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| |
Collapse
|
4
|
Wang L, Kulthinee S, Slate-Romano J, Zhao T, Shanmugam H, Dubielecka PM, Zhang LX, Qin G, Zhuang S, Chin YE, Zhao TC. Inhibition of integrin alpha v/beta 5 mitigates the protective effect induced by irisin in hemorrhage. Exp Mol Pathol 2023; 134:104869. [PMID: 37690529 PMCID: PMC10939993 DOI: 10.1016/j.yexmp.2023.104869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/27/2023] [Accepted: 09/06/2023] [Indexed: 09/12/2023]
Abstract
INTRODUCTION Irisin plays an important role in regulating tissue stress, cardiac function, and inflammation. Integrin αvβ5 was recently identified as a receptor for irisin to elicit its physiologic function. It remains unknown whether integrin αvβ5 is required for irisin's function in modulating the physiologic response to hemorrhage. The objective of this study is to examine if integrin αvβ5 contributes to the effects of irisin during the hemorrhagic response. METHODS Hemorrhage was induced in mice by achieving a mean arterial blood pressure of 35-45 mmHg for one hour, followed by two hours of resuscitation. Irisin (0.5 μg/kg) was administrated to assess its pharmacologic effects in hemorrhage. Cilengitide, a cyclic Arg-Gly-Asp peptide (cRGDyK) which is an inhibitor of integrin αvβ5, or control RGDS (1 mg/kg) was administered with irisin. In another cohort of mice, the irisin-induced protective effect was examined after knocking down integrin β5 with nanoparticle delivery of integrin β5 sgRNA using CRSIPR/Cas-9 gene editing. Cardiac function and hemodynamics were measured using echocardiography and femoral artery catheterization, respectively. Systemic cytokine releases were measured using Enzyme-linked immunosorbent assay (ELISA). Histological analyses were used to determine tissue damage in myocardium, skeletal muscles, and lung tissues. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) was carried out to assess apoptosis in tissues. RESULTS Hemorrhage induced reduction of integrin αvβ5 in skeletal muscles and repressed recovery of cardiac performance and hemodynamics. Irisin treatment led to significantly improved cardiac function, which was abrogated by treatment with Cilengitide or knockdown of integrin β5. Furthermore, irisin resulted in a marked suppression of tumor necrosis factor-α (TNF-α) and interleukin-1 (IL-1), muscle edema, and inflammatory cells infiltration in myocardium and skeletal muscles, which was attenuated by Cilengitide or knockdown of integrin β5. Irisin-induced reduction of apoptosis in the myocardium, skeletal muscles, and lung, which were attenuated by either the inhibition of integrin αvβ5, or knockdown of integrin β5. CONCLUSION Integrin αvβ5 plays an important role for irisin in modulating the protective effect during hemorrhage.
Collapse
Affiliation(s)
- Lijiang Wang
- Department of Plastic Surgery, Rhode Island Hospital, Brown University, USA
| | - Supaporn Kulthinee
- Department of Plastic Surgery, Rhode Island Hospital, Brown University, USA
| | - John Slate-Romano
- Department of Plastic Surgery, Rhode Island Hospital, Brown University, USA
| | | | - Hamsa Shanmugam
- Department of Plastic Surgery, Rhode Island Hospital, Brown University, USA
| | - Patrycja M Dubielecka
- Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Ling X Zhang
- Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Gangjian Qin
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shougang Zhuang
- Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | | | - Ting C Zhao
- Department of Plastic Surgery, Rhode Island Hospital, Brown University, USA; Department of Surgery, Rhode Island Hospital, Brown University, Providence, RI, USA.
| |
Collapse
|
5
|
Dai H, Zheng S, Zhang C, Huang R, Yuan L, Tong H. Identification and expression analysis of the KNOX genes during organogenesis and stress responseness in Camellia sinensis (L.) O. Kuntze. Mol Genet Genomics 2023; 298:1559-1578. [PMID: 37922102 DOI: 10.1007/s00438-023-02075-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 09/28/2023] [Indexed: 11/05/2023]
Abstract
Tea plant (Camellia sinensis L.), whose leaves are the major reproductive organs, has been cultivated and consumed widely for its economic and health benefits. The Knotted1-like Homeobox (KNOX) proteins play significant roles in leaf morphology formation and development. However, the functions of KNOX proteins in tea plants are still unknown. Here, 11 CsKNOX genes from the tea plants were cloned and divided into Class I, II, and KNATM clades based on their protein sequences. These 11 CsKNOX genes were mapped on 8 out of 15 tea plant chromosomes, all localized in the nucleus. Specific spatiotemporal expression patterns of CsKNOX genes were found in various tissues and different development periods of buds, flowers, and roots of tea plants. Meanwhile, transcript levels of CsKNOX in tea leaves were strongly correlated with the accumulation of flavan-3-ols and proanthocyanidins. It was found that most of the CsKNOX genes could respond to drought, salt, cold, and exogenous MeJA and GA3 by analysis of transcriptomics data and promoter elements. The protein interaction analysis showed that CsKNOX could cooperate with CsAS1 and other critical functional proteins. In conclusion, this research provided the basic information for the functions of the CsKNOX family during organogenesis and stress response in tea plants, which was necessary for further functional characterization verification.
Collapse
Affiliation(s)
- Hongwei Dai
- College of Food Science, Southwest University, Chongqing, 400715, People's Republic of China
| | - Shuting Zheng
- College of Food Science, Southwest University, Chongqing, 400715, People's Republic of China
| | - Cheng Zhang
- Nanchuan District's Agricultural Characteristic Industry Development Center of Chongqing Municipality, Chongqing, 408400, People's Republic of China
| | - Rui Huang
- College of Food Science, Southwest University, Chongqing, 400715, People's Republic of China
| | - Lianyu Yuan
- College of Food Science, Southwest University, Chongqing, 400715, People's Republic of China.
| | - Huarong Tong
- College of Food Science, Southwest University, Chongqing, 400715, People's Republic of China.
| |
Collapse
|
6
|
Megha S, Wang Z, Kav NNV, Rahman H. Genome-wide identification of biotin carboxyl carrier subunits of acetyl-CoA carboxylase in Brassica and their role in stress tolerance in oilseed Brassica napus. BMC Genomics 2022; 23:707. [PMID: 36253756 PMCID: PMC9578262 DOI: 10.1186/s12864-022-08920-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/23/2022] [Indexed: 11/22/2022] Open
Abstract
Background Biotin carboxyl carrier protein (BCCP) is a subunit of Acetyl CoA-carboxylase (ACCase) which catalyzes the conversion of acetyl-CoA to malonyl-CoA in a committed step during the de novo biosynthesis of fatty acids. Lipids, lipid metabolites, lipid-metabolizing and -modifying enzymes are known to play a role in biotic and abiotic stress tolerance in plants. In this regard, an understanding of the Brassica napus BCCP genes will aid in the improvement of biotic and abiotic stress tolerance in canola. Results In this study, we identified 43 BCCP genes in five Brassica species based on published genome data. Among them, Brassica rapa, Brassica oleracea, Brassica nigra, Brassica napus and Brassica juncea had six, seven, seven, 10 and 13 BCCP homologs, respectively. Phylogenetic analysis categorized them into five classes, each with unique conserved domains. The promoter regions of all BCCP genes contained stress-related cis-acting elements as determined by cis-element analysis. We identified four and three duplicated gene pairs (segmental) in B. napus and B. juncea respectively, indicating the role of segmental duplication in the expansion of this gene family. The Ka/Ks ratios of orthologous gene pairs between Arabidopsis thaliana and five Brassica species were mostly less than 1.0, implying that purifying selection, i.e., selective removal of deleterious alleles, played a role during the evolution of Brassica genomes. Analysis of 10 BnaBCCP genes using qRT-PCR showed a different pattern of expression because of exposure of the plants to biotic stresses, such as clubroot and sclerotinia diseases, and abiotic stresses such as drought, low temperature and salinity stresses. Conclusions The identification and functional analysis of the Brassica BCCPs demonstrated that some of these genes might play important roles in biotic and abiotic stress responses. Results from this study could lay the foundation for a better understanding of these genes for the improvement of Brassica crops for stress tolerance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08920-y.
Collapse
Affiliation(s)
- Swati Megha
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Zhengping Wang
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Nat N V Kav
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Habibur Rahman
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| |
Collapse
|
7
|
Chao N, Huang S, Kang X, Yidilisi K, Dai M, Liu L. Systematic functional characterization of cinnamyl alcohol dehydrogenase family members revealed their functional divergence in lignin biosynthesis and stress responses in mulberry. Plant Physiol Biochem 2022; 186:145-156. [PMID: 35849944 DOI: 10.1016/j.plaphy.2022.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/27/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Mulberry (Morus) is used as a feed additive and biofuel materials. Cinnamyl alcohol dehydrogenase (CAD; EC 1.1.1.95) catalyzes the final step of monolignol biosynthesis and is responsible for various monolignols. Five MaCADs from Morus alba were cloned and functionally characterized in the present study. These MaCADs encoded proteins with 357-364 amino acids, and the putative protein sequences conservatively possessed two Zn2+ binding motifs and an NADP(H) cofactor binding motif. However, MaCAD1, 2, and 5 shared similar amino acids at substrate binding positions that differed from those possessed by bona fide CADs. MaCAD3 and 4 had conservative substrate binding sites, and both phylogenetic and expression profile analysis indicated they were bona fide CADs involved in lignin biosynthesis. The enzymatic assay showed that MaCAD1 and 5 had a high affinity to p-coumaryl aldehyde. MaCAD4 preferentially used coniferyl aldehyde and sinapyl aldehyde as substrates. His-72 and Tyr-124 in MaCAD1 stabilized p-coumaryl aldehyde, and may have resulted in the substrate preference for p-coumaryl aldehyde. Down-regulation of MaCADs in mulberry showed that MaCAD3/4 were dominant CADs that functioned in monolignol biosynthesis, and decreased MaCAD3/4 resulted in significant decreases of lignin content in both stems and leaves. MaCADs exhibited different expression patterns in response to various stresses, indicating their possible diverse roles. MaCAD2 and MaCAD5 may play positive roles in response to drought and cold stresses, respectively. These results provide a systematic functional analysis of MaCADs in mulberry and an important foundation for the genetic modification of the monolignol pathway in mulberry.
Collapse
Affiliation(s)
- Nan Chao
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, 212018, China
| | - Shuai Huang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China
| | - Xiaoru Kang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China
| | - Keermula Yidilisi
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China
| | - Mingjie Dai
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China
| | - Li Liu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, 212018, China.
| |
Collapse
|
8
|
Felipez W, de Freitas KEJ, Dos Santos RS, Yamamoto RR, Costa de Oliveira A. The roles of WRKY transcription factors in Malus spp. and Pyrus spp. Funct Integr Genomics 2022. [PMID: 35906324 DOI: 10.1007/s10142-022-00886-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 11/04/2022]
Abstract
The WRKY transcription factor gene family is known to be involved in plant defense against pathogens and in tolerance to different environmental stresses at different stages of development. The response mechanisms through which these genes act can be influenced by different phytohormones as well as by many trans- and cis-acting elements, making this network an important topic for analysis, but still something complex to fully understand. According to available reports, these genes can also perform important roles in pome species (Malus spp. and Pyrus spp.) metabolism, especially in adaptation of these plants to stressful conditions. Here, we present a quick review of what is known about WRKY genes in Malus and Pyrus genomes offering a simple way to understand what is already known about this topic. We also add information connecting the evolution of these transcription factors with others that can also be found in pomes.
Collapse
|
9
|
Chimmani KV, Lokhande RD. Study the Behaviour of Underground Oil Cavern under Static Loading Condition. Geotech Geol Eng (Dordr) 2021; 40:995-1007. [PMID: 34776655 PMCID: PMC8294307 DOI: 10.1007/s10706-021-01939-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
The country's population is increasing rapidly and the need to make lives easier daily. Some of the essential needs for this generation are crude oil and electricity. India, unfortunately, does not possess any oil reserves to meet the needs of the country's demands. So, India is importing oil from other countries. Whenever there are situations like war, pandemic (COVID-19), and other emergencies, the natural oil reserved countries cannot export the oil to other countries which will lead to great chaos in the country. To avoid this situation storing the crude oil is necessary. Building surface giant structures for storing the oil is difficult and won't be economical. So, India is constructing giant underground structures called caverns, which will reserve the oil. The present study is focused on the stability of the underground cavern structure and understanding the importance of the water-curtaining system. To analyse the stresses and displacement 2D modelling has been done. In this, wet and dry models are prepared and analysed based on the available geological and geotechnical data to determine the stresses around the cavern and the displacement which will reach the surface due to excavation.
Collapse
Affiliation(s)
- K. V. Chimmani
- Department of Mining Engineering, VNIT Nagpur, Nagpur, Maharashtra India
| | - R. D. Lokhande
- Department of Mining Engineering, VNIT Nagpur, Nagpur, Maharashtra India
| |
Collapse
|
10
|
Zhao C, He L, Xia H, Zhou X, Geng Y, Hou L, Li P, Li G, Zhao S, Ma C, Tang R, Pandey MK, Varshney RK, Wang X. De novo full length transcriptome analysis of Arachis glabrata provides insights into gene expression dynamics in response to biotic and abiotic stresses. Genomics 2021; 113:1579-1588. [PMID: 33819563 DOI: 10.1016/j.ygeno.2021.03.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 03/21/2021] [Accepted: 03/29/2021] [Indexed: 11/26/2022]
Abstract
The perennial ornamental peanut Arachis glabrata represents one of the most adaptable wild Arachis species. This study used PacBio combined with BGISEQ-500 RNA-seq technology to study the transcriptome and gene expression dynamics of A. glabrata. Of the total 109,747 unique transcripts obtained, >90,566 transcripts showed significant homology to known proteins and contained the complete coding sequence (CDS). RNA-seq revealed that 1229, 1039, 1671, 3923, 1521 and 1799 transcripts expressed specifically in the root, stem, leaf, flower, peg and pod, respectively. We also identified thousands of differentially expressed transcripts in response to drought, salt, cold and leaf spot disease. Furthermore, we identified 30 polyphenol oxidase encoding genes associated with the quality of forage, making A. glabrata suitable as a forage crop. Our findings presented the first transcriptome study of A. glabrata which will facilitate genetic and genomics studies and lays the groundwork for a deeper understanding of the A. glabrata genome.
Collapse
Affiliation(s)
- Chuanzhi Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China; College of Life Sciences, Shandong Normal University, Jinan 250014, People's Republic of China.
| | - Liangqiong He
- Cash Crop Research Institute, Guangxi Academy of Agricultural Sciences, 530007 Nanning, People's Republic of China
| | - Han Xia
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China; College of Life Sciences, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Ximeng Zhou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China; College of Life Sciences, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Yun Geng
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China
| | - Lei Hou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China
| | - Pengcheng Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China; College of Life Sciences, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Guanghui Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China
| | - Shuzhen Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Ronghua Tang
- Cash Crop Research Institute, Guangxi Academy of Agricultural Sciences, 530007 Nanning, People's Republic of China
| | - Manish K Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, People's Republic of China; College of Life Sciences, Shandong Normal University, Jinan 250014, People's Republic of China.
| |
Collapse
|
11
|
Wangler J, Jansky M. Support, needs and expectations of family caregivers regarding general practitioners - results from an online survey. BMC Fam Pract 2021; 22:47. [PMID: 33658009 PMCID: PMC7927394 DOI: 10.1186/s12875-021-01381-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/28/2021] [Indexed: 11/10/2022]
Abstract
Background Family caregivers are often the first line of support for people requiring care; although they may personally stand to benefit, these activities substantially increase the risk of physical and emotional stress. General practitioners (GPs) may provide important support and stabilisation, but need to adjust to the needs and expectations of this group in order to do so. The aim of the study was to compare the needs of family caregivers from GPs to the support they actually experience. Additional aims included determining the main factors affecting satisfaction amongst family caregivers with support from GPs. The results were used to develop possible approaches towards optimisation within the purview of general medical practice. Methods Between January and July 2020, 612 people supporting or caring for a family member responded to an online survey posted in seventeen internet forums focused on family caregivers. In addition to the descriptive analysis, a t-test with independent samples was used to identify significant differences between two groups. We also used binary logistic regression analysis to identify indications of potentially influential factors regarding the experienced support from GPs. Results Around three out of every four respondents (72%) consulted GPs in care matters. The respondents gave positive responses on their GP’s knowledge of the care situation (71%), approachability in various issues connecting with care and service towards the caregiver (82%). GPs’ efforts in meeting the needs and requirements of the care recipient were also rated positively (82%). Weaknesses in support from GPs mainly involved the lack of information on advice and assistance services (55%) as well as frequently not identifying or involving caregivers as such soon enough (42%). Results from regression analysis show that the last two aspects play a major role in subjective satisfaction amongst family caregivers with support from GPs. Conclusions We recommend that GPs undergo further training to reinforce awareness that the care triad of needs, requirements and stresses amongst family caregivers also plays a vital role in care outcomes. With this in mind, general practice staff should adopt a pre-emptive strategy towards approaching family members about potential issues and informing them about existing assistance and support services. Supplementary Information The online version contains supplementary material available at 10.1186/s12875-021-01381-4.
Collapse
Affiliation(s)
- Julian Wangler
- Centre for General and Geriatric Medicine, University Medical Centre Mainz, Am Pulverturm 13, 55131, Mainz, Germany.
| | - Michael Jansky
- Centre for General and Geriatric Medicine, University Medical Centre Mainz, Am Pulverturm 13, 55131, Mainz, Germany
| |
Collapse
|
12
|
Butreddy A, Janga KY, Ajjarapu S, Sarabu S, Dudhipala N. Instability of therapeutic proteins - An overview of stresses, stabilization mechanisms and analytical techniques involved in lyophilized proteins. Int J Biol Macromol 2020; 167:309-325. [PMID: 33275971 DOI: 10.1016/j.ijbiomac.2020.11.188] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 01/06/2023]
Abstract
Solid-state is the preferred choice for storage of protein therapeutics to improve stability and preserve the biological activity by decreasing the physical and chemical degradation associated with liquid protein formulations. Lyophilization or freeze-drying is an effective drying method to overcome the instability problems of proteins. However, the processing steps (freezing, primary drying and secondary drying) involved in the lyophilization process can expose the proteins to various stress and harsh conditions, leading to denaturation, aggregation often a loss in activity of protein therapeutics. Stabilizers such as sugars and surfactants are often added to protect the proteins against physical stress associated with lyophilization process and storage conditions. Another way to curtail the degradation of proteins due to process related stress is by modification of the lyophilization process. Slow freezing, high nucleation temperature, decreasing the extent of supercooling, and annealing can minimize the formation of the interface (ice-water) by producing large ice crystals with less surface area, thereby preserving the native structure and stability of the proteins. Hence, a thorough understanding of formulation composition, lyophilization process parameters and the choice of analytical methods to characterize and monitor the protein instability is crucial for development of stable therapeutic protein products. This review provides an overview of various stress conditions that proteins might encounter during lyophilization process, mechanisms to improve the stability and analytical techniques to tackle the proteins instability during both freeze-drying and storage.
Collapse
Affiliation(s)
- Arun Butreddy
- Formulation R&D, Biological E. Limited, IKP Knowledge Park, Shameerpet, Hyderabad, Telangana State 500078, India; Laboratory of Nanotechnology, University College of Pharmaceutical Sciences, Kakatiya University, Warangal, Telangana State 506009, India
| | - Karthik Yadav Janga
- Laboratory of Nanotechnology, University College of Pharmaceutical Sciences, Kakatiya University, Warangal, Telangana State 506009, India
| | - Srinivas Ajjarapu
- Industrial Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science, Pilani 333031, India
| | - Sandeep Sarabu
- Laboratory of Nanotechnology, University College of Pharmaceutical Sciences, Kakatiya University, Warangal, Telangana State 506009, India
| | - Narendar Dudhipala
- Laboratory of Nanotechnology, University College of Pharmaceutical Sciences, Kakatiya University, Warangal, Telangana State 506009, India; Department of Pharmaceutics, Vaagdevi College of Pharmacy, Warangal, Telangana State 506 005, India..
| |
Collapse
|
13
|
Zaman Khan N, Lal S, Ali W, Aasim M, Mumtaz S, Kamil A, Shad Bibi N. Distribution and Classification of Dehydrins in Selected Plant Species Using Bioinformatics Approach. Iran J Biotechnol 2020; 18:e2680. [PMID: 34056027 PMCID: PMC8148643 DOI: 10.30498/ijb.2020.2680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Background: Plant growth, reproduction and yields are severely damaged under adverse environmental stresses. These stresses can be either biotic or abiotic, and many stress related proteins are expressed in response to these stresses. Among these proteins dehydrins are reported to have a role primarily in the abiotic stresses. Dehydrins are very diverse proteins and a uniform annotation system is needed for their functional characterization in the future research. Objectives: The aim of the present work is to identify, classify and analyze the expression of dehydrin proteins under different biotic and abiotic stresses in the selected plant species by using different computational tools. Materials and Methods: Prosite database is used for dehydrin proteins identification, and to conform the location of conserved motifs in selected plant species. The dehydrins extracted from uniprot database were annotated, based on the ensemble plant gene id. Subcellular localization was predicted using PSI predictor tool. Dehydrin expression analyses were retrieved form the genevestigator tool. Results: Dehydrins were annotated on the basis of dehydrin gene locus and conserved motifs available in different domain databases.
Dehydrins were identified and annotated in Arabidopsis thaliana (13), Glycine max (12), Zea mays (05),
Oryza sativa (11), Solanum tuberosum (05), Solanum lycopersicum (06), Triticum aestivum (32)
and Vitis vinifera (06). It has been proposed that dehydrins are located primarily in cytosol
and nucleus. Based on genevestigater expression analyses the plant species selected for this study contain all the
classes of dehydrins, namely YnSKn, Kn, SKn, and YnKn; except class KnS. Conclusions: Dehydrins are diverse proteins and a uniform classification is introduced for their better characterization.
The distribution of dehydrins in different tissues and developmental stages suggest an important function throughout
plant growth cycle. It has also been concluded that dehydrins expressed particularly in drought, cold and salt stresses,
and may have limited role in heat, anoxia, heavy-metal and biotic stresses as well.
Collapse
Affiliation(s)
- Nadir Zaman Khan
- Department of Biotechnology, University of Malakand, Chakdara, Lower Dir, Pakistan
| | - Shahzadi Lal
- Department of Biotechnology, University of Malakand, Chakdara, Lower Dir, Pakistan
| | - Waqar Ali
- Department of Biotechnology, University of Malakand, Chakdara, Lower Dir, Pakistan
| | - Muhammad Aasim
- Department of Biotechnology, University of Malakand, Chakdara, Lower Dir, Pakistan
| | - Saqib Mumtaz
- Department of Biosciences, COMSAT University, Islamabad, Pakistan
| | - Atif Kamil
- Department of Biotechnology, Abdul Wali Khan University Mardan, Pakistan
| | - Noor Shad Bibi
- Department of Biochemistry, Abdul Wali Khan University Mardan, Pakistan
| |
Collapse
|
14
|
Yin J, Wang L, Zhao J, Li Y, Huang R, Jiang X, Zhou X, Zhu X, He Y, He Y, Liu Y, Zhu Y. Genome-wide characterization of the C2H2 zinc-finger genes in Cucumis sativus and functional analyses of four CsZFPs in response to stresses. BMC Plant Biol 2020; 20:359. [PMID: 32727369 PMCID: PMC7392682 DOI: 10.1186/s12870-020-02575-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/23/2020] [Indexed: 05/25/2023]
Abstract
BACKGROUNDS C2H2-type zinc finger protein (ZFPs) form a relatively large family of transcriptional regulators in plants, and play many roles in plant growth, development, and stress response. However, the comprehensive analysis of C2H2 ZFPs in cucumber (CsZFPs) and their regulation function in cucumber are still lacking. RESULTS In the current study, the whole genome identification and characterization of CsZFPs, including the gene structure, genome localization, phylogenetic relationship, and gene expression were performed. Functional analysis of 4 selected genes by transient transformation were also conducted. A total of 129 full-length CsZFPs were identified, which could be classified into four groups according to the phylogenetic analysis. The 129 CsZFPs unequally distributed on 7 chromosomes. Promoter cis-element analysis showed that the CsZFPs might involve in the regulation of phytohormone and/or abiotic stress response, and 93 CsZFPs were predicted to be targeted by one to 20 miRNAs. Moreover, the subcellular localization analysis indicated that 10 tested CsZFPs located in the nucleus and the transcriptome profiling analysis of CsZFPs demonstrated that these genes are involved in root and floral development, pollination and fruit spine. Furthermore, the transient overexpression of Csa1G085390 and Csa7G071440 into Nicotiana benthamiana plants revealed that they could decrease and induce leave necrosis in response to pathogen attack, respectively, and they could enhance salt and drought stresses through the initial induction of H2O2. In addition, Csa4G642460 and Csa6G303740 could induce cell death after 5 days transformation. CONCLUSIONS The identification and function analysis of CsZFPs demonstrated that some key individual CsZFPs might play essential roles in response to biotic and abiotic stresses. These results could lay the foundation for understanding the role of CsZFPs in cucumber development for future genetic engineering studies.
Collapse
Affiliation(s)
- Junliang Yin
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
| | - Lixin Wang
- College of Horticulture, Hebei Agricultural University, Baoding, 071001 Hebei China
| | - Jiao Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, 071001 Hebei China
| | - Yiting Li
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
| | - Rong Huang
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
| | - Xinchen Jiang
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434000 Hubei China
| | - Xiaokang Zhou
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434000 Hubei China
| | - Xiongmeng Zhu
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434000 Hubei China
| | - Yang He
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434000 Hubei China
| | - Yiqin He
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
| | - Yiqing Liu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434000 Hubei China
| | - Yongxing Zhu
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434000 Hubei China
| |
Collapse
|
15
|
Wang L, Li M, Liu Z, Dai L, Zhang M, Wang L, Zhao J, Liu M. Genome-wide identification of CNGC genes in Chinese jujube (Ziziphus jujuba Mill.) and ZjCNGC2 mediated signalling cascades in response to cold stress. BMC Genomics 2020; 21:191. [PMID: 32122304 DOI: 10.1186/s12864-020-6601-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 02/20/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUNDS Cyclic nucleotide gated channels (CNGCs) play multifaceted roles in plant physiological processes, especially with respect to signalling processes, plant development, and responses to environmental stresses. However, little information is known about the CNGC family in the large cosmopolitan family Rhamnaceae, which has strong tolerance to biotic and abiotic stresses. RESULTS In the current study, a total of 15 ZjCNGCs which located on 7 chromosomes were firstly identified in Chinese jujube (Ziziphus jujuba Mill.), the most important species of Rhamnaceae in terms of economic and ecological values. Phylogenetic analysis showed that these ZjCNGCs could be classified into four groups, ZjCNGC12 belonged to group IVA, and ZjCNGC13, 14, 15 belonged to group IVB. In addition, the paralogous and orthologous homology duplication of ZjCNGC15 occurred during the evolutionary process. The characteristics of ZjCNGCs regarding to exon-intron numbers and post-translational modifications showed diversified structures and functions. Motif composition and protein sequence analysis revealed that the phosphate-binding cassette and hinge regions were conserved among ZjCNGCs. Prediction of the cis-acting regulatory elements and expression profiles by real-time quantitative PCR analysis showed that some of the ZjCNGCs responded to environmental changes, especially ZjCNGC2, which was significantly downregulated in response to cold stress, and ZjCNGC4 was highly induced in response to cold, salt and alkaline stresses. ZjCNGC13 and 14 were highly induced in the phytoplasma-resistant cultivar and downregulated in the susceptible cultivar. Furthermore, ZjCNGC2 could be regulated by cAMP treatment, microtubule changes and interact with ZjMAPKK4, which suggested that cAMP and microtubule might play important roles in ZjCNGC2 mediated ZjMAPKK4 signalling transduction involved in cold stress. CONCLUSIONS The identification and classification analysis of ZjCNGCs were firstly reported, and some key individual ZjCNGCs might play essential roles in the response to biotic and abiotic stresses, especially ZjCNGC2 mediated ZjMAPKK4 signalling transduction involved in cold stress. This systematic analysis could provide important information for further functional characterization of ZjCNGCs with the aim of breeding stress-resistant cultivars.
Collapse
|
16
|
Abedini D, Rashidi Monfared S. Co-regulation analysis of co-expressed modules under cold and pathogen stress conditions in tomato. Mol Biol Rep 2018; 45:335-345. [PMID: 29551007 DOI: 10.1007/s11033-018-4166-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/13/2018] [Indexed: 11/28/2022]
Abstract
A primary mechanism for controlling the development of multicellular organisms is transcriptional regulation, which carried out by transcription factors (TFs) that recognize and bind to their binding sites on promoter region. The distance from translation start site, order, orientation, and spacing between cis elements are key factors in the concentration of active nuclear TFs and transcriptional regulation of target genes. In this study, overrepresented motifs in cold and pathogenesis responsive genes were scanned via Gibbs sampling method, this method is based on detection of overrepresented motifs by means of a stochastic optimization strategy that searches for all possible sets of short DNA segments. Then, identified motifs were checked by TRANSFAC, PLACE and Soft Berry databases in order to identify putative TFs which, interact to the motifs. Several cis/trans regulatory elements were found using these databases. Moreover, cross-talk between cold and pathogenesis responsive genes were confirmed. Statistical analysis was used to determine distribution of identified motifs on promoter region. In addition, co-regulation analysis results, illustrated genes in pathogenesis responsive module are divided into two main groups. Also, promoter region was crunched to six subareas in order to draw the pattern of distribution of motifs in promoter subareas. The result showed the majority of motifs are concentrated on 700 nucleotides upstream of the translational start site (ATG). In contrast, this result isn't true in another group. In other words, there was no difference between total and compartmentalized regions in cold responsive genes.
Collapse
Affiliation(s)
- Davar Abedini
- Department of Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Sajad Rashidi Monfared
- Department of Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| |
Collapse
|
17
|
Zubairi A, Rashid RH, Zahid M, Hashmi PM, Noordin S. Proximal Femur Locking Plate for Sub-Trochanteric Femur Fractures: Factors Associated with Failure. Open Orthop J 2017; 11:1058-1065. [PMID: 28979608 PMCID: PMC5612058 DOI: 10.2174/1874325001711011058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/06/2017] [Accepted: 08/04/2017] [Indexed: 11/22/2022] Open
Abstract
Introduction: Proximal femur locking compression plates (PF-LCP) have gained popularity since their inception due to superior biomechanical stability and durability but clinical experience has shown conflicting results including implant failure. Objective: To study the incidence of implant failure in patients with sub-trochanteric fractures managed with proximal femoral locking compression plate and identify potential risk factors associated with the failure. Materials & Methods: Fifty patients with sub-trochanteric fractures, operated upon with titanium PF-LCP were included in the study from January 2012 to December 2014. These plates were of two designs including one five 5.0 mm proximal locking screws (implant A) and other with three 6.5 mm proximal locking screws (implant B). Fractures were classified according to AO/OTA and Seinsheimer classification. Patients had regular follow-up visits for at least a year, allowing for clinical and radiological assessment of union and implant-related complications. Results: A total of 13 out of 50 (26%) plates failed of which 7 were implant fractures, 3 screw breakage and 3 screw cut outs. 70% of the failures occurred in elderly females. Overall implant failure was significantly more common in patients >50 years (p 0.04). Comparing the two different designs of implants used, implant A was more likely to fail at a plate screw density of 0.8 or more (p 0.02), whereas implant B was associated with significant failure when less than 4 proximal screws were used (p 0.03). Conclusion: This study revealed a high failure rate (26%) of this implant. Attention to the neck shaft angle difference, number of proximal screws and plate screw density may help reduce failure rates, particularly in elderly osteoporotic females.
Collapse
Affiliation(s)
- Akbar Zubairi
- Section of Orthopedics, Aga Khan University Hospital, Karachi, Pakistan
| | | | - Marij Zahid
- Section of Orthopedics, Aga Khan University Hospital, Karachi, Pakistan
| | | | - Shahryar Noordin
- Section of Orthopedics, Aga Khan University Hospital, Karachi, Pakistan
| |
Collapse
|
18
|
Reis VR, Antonangelo ATBF, Bassi APG, Colombi D, Ceccato-Antonini SR. Bioethanol strains of Saccharomyces cerevisiae characterised by microsatellite and stress resistance. Braz J Microbiol 2017; 48:268-74. [PMID: 28057426 DOI: 10.1016/j.bjm.2016.09.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 09/19/2016] [Indexed: 11/22/2022] Open
Abstract
Strains of Saccharomyces cerevisiae may display characteristics that are typical of rough-type colonies, made up of cells clustered in pseudohyphal structures and comprised of daughter buds that do not separate from the mother cell post-mitosis. These strains are known to occur frequently in fermentation tanks with significant lower ethanol yield when compared to fermentations carried out by smooth strains of S. cerevisiae that are composed of dispersed cells. In an attempt to delineate genetic and phenotypic differences underlying the two phenotypes, this study analysed 10 microsatellite loci of 22 S. cerevisiae strains as well as stress resistance towards high concentrations of ethanol and glucose, low pH and cell sedimentation rates. The results obtained from the phenotypic tests by Principal-Component Analysis revealed that unlike the smooth colonies, the rough colonies of S. cerevisiae exhibit an enhanced resistance to stressful conditions resulting from the presence of excessive glucose and ethanol and high sedimentation rate. The microsatellite analysis was not successful to distinguish between the colony phenotypes as phenotypic assays. The relevant industrial strain PE-2 was observed in close genetic proximity to rough-colony although it does not display this colony morphology. A unique genetic pattern specific to a particular phenotype remains elusive.
Collapse
|
19
|
Hong HK, Donaghy L, Kang CK, Kang HS, Lee HJ, Park HS, Choi KS. Substantial changes in hemocyte parameters of Manila clam Ruditapes philippinarum two years after the Hebei Spirit oil spill off the west coast of Korea. Mar Pollut Bull 2016; 108:171-179. [PMID: 27132991 DOI: 10.1016/j.marpolbul.2016.04.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 04/09/2016] [Accepted: 04/14/2016] [Indexed: 06/05/2023]
Abstract
Two years after the Hebei Spirit oil spill occurred off the west coast of Korea, we determined sub-lethal effects of the spilled oil on hemocyte parameters of Ruditapes philippinarum in the damaged areas. Clams in the spilled sites displayed unusually high proportion of granulocytes, which may result in higher phagocytosis capacity and reactive oxygen species production. Hemocytes in clams from the polluted sites also displayed less DNA damage and mortality than in the control site, possibly due to a faster phagocytosis of the impaired cells. Glycogen, the major energetic reserve, was depleted in clams from the spilled sites, potentially due to energetic consumption for maintenance of a large pool of granulocytes, detoxification processes and oxidative stress. Modified hemocyte parameters in clams in the spilled area, may reflect sub-lethal physiological stresses caused by the residual oils in the sediment, in conjunction with environmental modifications such as food availability and pathogens pattern.
Collapse
Affiliation(s)
- Hyun-Ki Hong
- School of Marine Biomedical Science (BK21 PLUS), Jeju National University 102, Jejudaehakno, Jeju 690-756, Republic of Korea
| | - Ludovic Donaghy
- School of Marine Biomedical Science (BK21 PLUS), Jeju National University 102, Jejudaehakno, Jeju 690-756, Republic of Korea
| | - Chang-Keun Kang
- School of Environmental Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Hyun-Sil Kang
- School of Marine Biomedical Science (BK21 PLUS), Jeju National University 102, Jejudaehakno, Jeju 690-756, Republic of Korea
| | - Hee-Jung Lee
- School of Marine Biomedical Science (BK21 PLUS), Jeju National University 102, Jejudaehakno, Jeju 690-756, Republic of Korea
| | - Heung-Sik Park
- Marine Ecosystem and Environment Research Division, Korea Institute of Ocean Science and Technology (KIOST), Ansan 425-600, Republic of Korea
| | - Kwang-Sik Choi
- School of Marine Biomedical Science (BK21 PLUS), Jeju National University 102, Jejudaehakno, Jeju 690-756, Republic of Korea.
| |
Collapse
|
20
|
Wang X, Komatsu S. Plant subcellular proteomics: Application for exploring optimal cell function in soybean. J Proteomics 2016; 143:45-56. [PMID: 26808589 DOI: 10.1016/j.jprot.2016.01.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/06/2016] [Accepted: 01/13/2016] [Indexed: 01/11/2023]
Abstract
UNLABELLED Plants have evolved complicated responses to developmental changes and stressful environmental conditions. Subcellular proteomics has the potential to elucidate localized cellular responses and investigate communications among subcellular compartments during plant development and in response to biotic and abiotic stresses. Soybean, which is a valuable legume crop rich in protein and vegetable oil, can grow in several climatic zones; however, the growth and yield of soybean are markedly decreased under stresses. To date, numerous proteomic studies have been performed in soybean to examine the specific protein profiles of cell wall, plasma membrane, nucleus, mitochondrion, chloroplast, and endoplasmic reticulum. In this review, methods for the purification and purity assessment of subcellular organelles from soybean are summarized. In addition, the findings from subcellular proteomic analyses of soybean during development and under stresses, particularly flooding stress, are presented and the proteins regulated among subcellular compartments are discussed. Continued advances in subcellular proteomics are expected to greatly contribute to the understanding of the responses and interactions that occur within and among subcellular compartments during development and under stressful environmental conditions. BIOLOGICAL SIGNIFICANCE Subcellular proteomics has the potential to investigate the cellular events and interactions among subcellular compartments in response to development and stresses in plants. Soybean could grow in several climatic zones; however, the growth and yield of soybean are markedly decreased under stresses. Numerous proteomics of cell wall, plasma membrane, nucleus, mitochondrion, chloroplast, and endoplasmic reticulum was carried out to investigate the respecting proteins and their functions in soybean during development or under stresses. In this review, methods of subcellular-organelle enrichment and purity assessment are summarized. In addition, previous findings of subcellular proteomics are presented, and functional proteins regulated among different subcellular are discussed. Subcellular proteomics contributes greatly to uncovering responses and interactions among subcellular compartments during development and under stressful environmental conditions in soybean.
Collapse
Affiliation(s)
- Xin Wang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
| |
Collapse
|
21
|
Palusa SG, Reddy ASN. Differential recruitment of splice variants from SR pre-mRNAs to polysomes during development and in response to stresses. Plant Cell Physiol 2015; 56:421-7. [PMID: 25637375 DOI: 10.1093/pcp/pcv010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We have previously shown that precursor mRNAs (pre-mRNAs) of serine/arginine-rich (SR) proteins are extensively alternatively spliced to generate approximately 100 distinct splice variants from 14 SR genes and that the splicing pattern of SR pre-mRNAs changes in different organs and in response to abiotic stresses. About half of the splice variants are potential targets of nonsense-mediated decay (NMD) and 25 splice forms were confirmed to be real NMD targets. However, it is not known whether (i) all splice variants are recruited to polysomes for translation; (ii) there is a preferential recruitment of specific splice isoforms to polysomes; and (iii) there is a differential recruitment of splice variants during development and in response to stresses. To address these questions, we analyzed the association of SR splice variants with polysomes from seedlings, different organs and seedlings exposed to heat and cold stress. In seedlings, about one-third of the splice variants (22 out of 72) are not recruited to polysomes. Among those associated with polysomes, the functional isoforms that code for full-length proteins and some candidate putative and confirmed NMD targets were identified. There was preferential recruitment of some splice forms over others. Predominant recruitment of functional isoforms along with a few NMD candidates was found in different organs. Furthermore, we observed differential recruitment of isoforms in different organs. Heat and cold stress enhanced or reduced recruitment of specific splice variants. Our studies reveal differential recruitment of SR splice variants to polysomes under normal conditions, during development and in response to stresses.
Collapse
Affiliation(s)
- Saiprasad Goud Palusa
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Anireddy S N Reddy
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| |
Collapse
|
22
|
Shrivastava A, Hazarey PV, Kharbanda OP, Gupta A. Stress distribution in the temporomandibular joint after mandibular protraction: a three-dimensional finite element study. Angle Orthod 2015; 85:196-205. [PMID: 24901066 PMCID: PMC8631882 DOI: 10.2319/091913-690.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 04/01/2014] [Indexed: 10/17/2023] Open
Abstract
OBJECTIVE To evaluate the stress patterns in temporomandibular joint (TMJ) during mandibular protraction at different horizontal advancements with constant vertical height in a construction bite using a three-dimensional finite element method. MATERIALS AND METHODS A three-dimensional computer-aided model was developed from the magnetic resonance imaging (MRI) of a growing boy (age 12 years) using MIMICS software (version 7.0, Materialise, Leuven, Belgium). Stresses with constant vertical opening of 5 mm changing the sagittal advancements from 0 mm to 5 mm and 7.5 mm were recorded. Differences in magnitude and pattern of stresses were compared. RESULTS The tensile stresses in the posterosuperior aspect of the condylar head and on the posterior aspect of the glenoid fossa migrated posteriorly with increased bite advancements. The location of tensile stresses changed in the condylar head and fossa on mandibular protraction of 5 mm to 7 mm. CONCLUSION This study indicates that larger horizontal advancements of construction bites may not be favorable for tissues of TMJ. Clinical application necessitates study on an animal model.
Collapse
Affiliation(s)
- Abhinav Shrivastava
- Senior Lecturer, Department of Orthodontics, Hitkarni Dental College, Jabalpur, India
| | - Pushpa V Hazarey
- Professor and Head, Department of Orthodontics, Sharad Pawar Dental College, Wardha, India
| | - Om P. Kharbanda
- Professor and Head, Department of Orthodontics and Dentofacial Deformities, Centre for Dental Excellence and Research, All India Institute of Medical Sciences, New Delhi, India
| | - Anurag Gupta
- Head Consultant, Maximus Specialist Centre for Dental Research, New Delhi, India
| |
Collapse
|
23
|
Roberts RM, Muller T, Sweeney A, Bratkovic D, Gannoni A. Promoting psychological well-being in women with phenylketonuria: Pregnancy-related stresses, coping strategies and supports. Mol Genet Metab Rep 2014; 1:148-157. [PMID: 27896085 PMCID: PMC5121318 DOI: 10.1016/j.ymgmr.2014.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 03/18/2014] [Indexed: 10/27/2022] Open
Abstract
OBJECTIVE To explore the pregnancy-related stresses anticipated and experienced by women with phenylketonuria (PKU) and the coping strategies and supports utilised or anticipated to be beneficial during pregnancy. METHODS Thematic analysis of interview data from eight women with PKU in a cross-sectional, qualitative study. Five of the participants had never had a pregnancy but were planning to in the future, two participants had children, and one participant was pregnant. RESULTS The central concern regarding pregnancy was achieving and maintaining the essential low Phe levels, in the context of the devastating effects of high levels. The Transactional Model of Stress and Coping was utilised to understand the coping strategies and supports utilised or anticipated to be beneficial during pregnancy. Similarities and differences between the women who had experienced pregnancy, and those who were planning a pregnancy in the future were evident in key coping strategies, with knowledge seeking, positive reappraisal, and reassurance seeking reported. Support from health professionals and other mothers with PKU was key for all women. Psychological support was identified as a resource perceived to be beneficial to promote psychological well-being during pregnancy but not yet provided. CONCLUSION Pregnancy is associated with significant stresses for women with PKU. Clinical implications of the findings include provision of psychological support.
Collapse
Affiliation(s)
| | - Tamara Muller
- School of Psychology, University of Adelaide, Adelaide, Australia
| | - Annabel Sweeney
- Department of Nutrition, Women's and Children's Hospital, Adelaide, Australia
| | - Drago Bratkovic
- Metabolic Unit, Women's and Children's Hospital, Adelaide, Australia
| | - Anne Gannoni
- Department of Psychological Medicine, Women's and Children's Hospital, Adelaide, Australia
| |
Collapse
|
24
|
Agostini S, Fujimura H, Higuchi T, Yuyama I, Casareto BE, Suzuki Y, Nakano Y. The effects of thermal and high-CO2 stresses on the metabolism and surrounding microenvironment of the coral Galaxea fascicularis. C R Biol 2013; 336:384-91. [PMID: 24018195 DOI: 10.1016/j.crvi.2013.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 04/09/2013] [Accepted: 07/23/2013] [Indexed: 12/01/2022]
Abstract
The effects of elevated temperature and high pCO2 on the metabolism of Galaxea fascicularis were studied with oxygen and pH microsensors. Photosynthesis and respiration rates were evaluated from the oxygen fluxes from and to the coral polyps. High-temperature alone lowered both photosynthetic and respiration rates. High pCO2 alone did not significantly affect either photosynthesis or respiration rates. Under a combination of high-temperature and high-CO2, the photosynthetic rate increased to values close to those of the controls. The same pH in the diffusion boundary layer was observed under light in both (400 and 750 ppm) CO2 treatments, but decreased significantly in the dark as a result of increased CO2. The ATP contents decreased with increasing temperature. The effects of temperature on the metabolism of corals were stronger than the effects of increased CO2. The effects of acidification were minimal without combined temperature stress. However, acidification combined with higher temperature may affect coral metabolism due to the amplification of diel variations in the microenvironment surrounding the coral and the decrease in ATP contents.
Collapse
Affiliation(s)
- Sylvain Agostini
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, 1 Senbaru, Nishihara-cho, 903-0213 Okinawa, Japan; Shimoda Marine Research Center, Tsukuba University, 5-10-1, Shimoda, 415-0025 Shizuoka, Japan.
| | | | | | | | | | | | | |
Collapse
|