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Lu Y, Ma Y, Li B, Sun H. The biogenesis, identification, and functionality of circWWP2 in lipopolysaccharide stimulated macrophages. Gene 2024; 905:148240. [PMID: 38316263 DOI: 10.1016/j.gene.2024.148240] [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: 11/09/2023] [Revised: 01/23/2024] [Accepted: 01/31/2024] [Indexed: 02/07/2024]
Abstract
CircRNA, a non-coding RNA, is an ideal biomarker and a suitable potential therapeutic target for various disease due to its high stability, species conservation and cell/tissue specificity. Our previous study has found a circular RNA WWP2 (circWWP2) was significantly decreased in chicken macrophages during bacterial infection. However, the function of circWWP2 in chicken macrophages remains unclear. In this study, it was demonstrated that circWWP2 was a stable circular RNA created by back-splicing of exons 2 to 4 of WWP2 via PCR amplification, Sanger sequencing, RNase R exonuclease digestion, and RT-qPCR. Moreover, bioinformatics analysis showed circWWP2 could interact with 13 miRNAs and target 3,264 genes, which were significantly enriched in lysosomes, IgA-producing intestinal immune networks for IgA production, and Notch signaling pathway. Furthermore, CCK8 and RT-qPCR indicated that overexpression of circWWP2 could promote lipopolysaccharide (LPS)-induced cellular injury by decreasing cell viability and increasing the expression levels of pro-inflammatory cytokines and pro-apoptosis genes, and NO production. CircWWP2 may exert a potential target for the treatment of bacterial infection. Further experiments are necessary to validate the specific mechanism that circWWP2 regulates LPS induced cellular immune responses.
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Affiliation(s)
- Yue Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yuyi Ma
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Bichun Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Hongyan Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
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2
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van Nuland TDH. Noncompact uniform universal approximation. Neural Netw 2024; 173:106181. [PMID: 38412737 DOI: 10.1016/j.neunet.2024.106181] [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: 08/04/2023] [Revised: 12/28/2023] [Accepted: 02/13/2024] [Indexed: 02/29/2024]
Abstract
The universal approximation theorem is generalised to uniform convergence on the (noncompact) input space Rn. All continuous functions that vanish at infinity can be uniformly approximated by neural networks with one hidden layer, for all activation functions φ that are continuous, nonpolynomial, and asymptotically polynomial at ±∞. When φ is moreover bounded, we exactly determine which functions can be uniformly approximated by neural networks, with the following unexpected results. Let Nφl(Rn)¯ denote the vector space of functions that are uniformly approximable by neural networks with l hidden layers and n inputs. For all n and all l≥2, Nφl(Rn)¯ turns out to be an algebra under the pointwise product. If the left limit of φ differs from its right limit (for instance, when φ is sigmoidal) the algebra Nφl(Rn)¯ (l≥2) is independent of φ and l, and equals the closed span of products of sigmoids composed with one-dimensional projections. If the left limit of φ equals its right limit, Nφl(Rn)¯ (l≥1) equals the (real part of the) commutative resolvent algebra, a C*-algebra which is used in mathematical approaches to quantum theory. In the latter case, the algebra is independent of l≥1, whereas in the former case Nφ2(Rn)¯ is strictly bigger than Nφ1(Rn)¯.
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Vanderhout RJ, Abdalla EA, Leishman EM, Barbut S, Wood BJ, Baes CF. Genetic architecture of white striping in turkeys (Meleagris gallopavo). Sci Rep 2024; 14:9007. [PMID: 38637585 PMCID: PMC11026500 DOI: 10.1038/s41598-024-59309-8] [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: 11/17/2023] [Accepted: 04/09/2024] [Indexed: 04/20/2024] Open
Abstract
White striping (WS) is a myopathy of growing concern to the turkey industry. It is rising in prevalence and has negative consequences for consumer acceptance and the functional properties of turkey meat. The objective of this study was to conduct a genome-wide association study (GWAS) and functional analysis on WS severity. Phenotypic data consisted of white striping scored on turkey breast fillets (N = 8422) by trained observers on a 0-3 scale (none to severe). Of the phenotyped birds, 4667 genotypic records were available using a proprietary 65 K single nucleotide polymorphism (SNP) chip. The SNP effects were estimated using a linear mixed model with a 30-SNP sliding window approach used to express the percentage genetic variance explained. Positional candidate genes were those located within 50 kb of the top 1% of SNP windows explaining the most genetic variance. Of the 95 positional candidate genes, seven were further classified as functional candidate genes because of their association with both a significant gene ontology and molecular function term. The results of the GWAS emphasize the polygenic nature of the trait with no specific genomic region contributing a large portion to the overall genetic variance. Significant pathways relating to growth, muscle development, collagen formation, circulatory system development, cell response to stimulus, and cytokine production were identified. These results help to support published biological associations between WS and hypoxia and oxidative stress and provide information that may be useful for future-omics studies in understanding the biological associations with WS development in turkeys.
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Affiliation(s)
- Ryley J Vanderhout
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Hybrid Turkeys, 650 Riverbend Drive Suite C, Kitchener, ON, N2K 3S2, Canada
| | - Emhimad A Abdalla
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Vereinigte Informationssysteme Tierhaltung W.V. (Vit), Heinrich-Schröder-Weg 1, 27283, Verden, Germany
| | - Emily M Leishman
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Shai Barbut
- Department of Food Science, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Benjamin J Wood
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Hybrid Turkeys, 650 Riverbend Drive Suite C, Kitchener, ON, N2K 3S2, Canada
- School of Veterinary Science, University of Queensland, Gatton, QLD, 4343, Australia
| | - Christine F Baes
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.
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Cai X, Song Q, Meng X, Li K, Shi S, Jin L, Kan H, Wang S. Epigenome-wide association study on ambient PM 2.5 exposure in Han Chinese, the NSPT study. Environ Res 2024; 247:118276. [PMID: 38246299 DOI: 10.1016/j.envres.2024.118276] [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: 10/10/2023] [Revised: 01/02/2024] [Accepted: 01/18/2024] [Indexed: 01/23/2024]
Abstract
Ambient PM2.5 exposure has been recognized as a major health risk and related to aging, cardiovascular, respiratory and neurologic diseases, and cancer. However, underlying mechanism of epigenetic alteration and regulated pathways still remained unclear. The study on methylome effect of PM2.5 exposure was quite limited in Chinese population, and cohort-based study was absent. The study included blood-derived DNA methylation for 3365 Chinese participants from the NSPT cohort. We estimated individual PM2.5 exposure level of short-medium-, medium- and long-term, based on a validated prediction model. We preformed epigenome-wide association studies to estimate the links between PM2.5 exposure and DNA methylation change, as well as stratification and sensitive analysis to examined the robustness of the association models. A systematic review was conducted to obtain the previously published CpGs and examined for replication. We also conducted comparison on the DNA methylation variation corresponding to different time windows. We further conducted gene function analysis and pathway enrichment analysis to reveal related biological response. We identified a total of 177 CpGs and 107 DMRs associated with short-medium-term PM2.5 exposure, at a strict genome-wide significance (P < 5 × 10-8). The effect sizes on most CpGs tended to cease with the exposure of extended time scale. Associated markers and aligned genes were related to aging, immunity, inflammation and carcinogenesis. Enriched pathways were mostly involved in cell cycle and cell division, signal transduction, inflammatory pathway. Our study is the first EWAS on PM2.5 exposure conducted in large-scale Han Chinese cohort and identified associated DNA methylation change on CpGs and regions, as well as related gene functions and pathways.
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Affiliation(s)
- Xiyang Cai
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qinglin Song
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xia Meng
- School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai, 200032, China
| | - Kaixuan Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Su Shi
- School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai, 200032, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, and Human Phenome Institute, Fudan University, Shanghai, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China; Taizhou Institute of Health Sciences, Fudan University, Taizhou, Jiangsu, China
| | - Haidong Kan
- School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai, 200032, China; Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, 201102, China.
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China; Taizhou Institute of Health Sciences, Fudan University, Taizhou, Jiangsu, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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Chu WC, Gao YY, Wu YX, Liu FF. Biofilm of petroleum-based and bio-based microplastics in seawater in response to Zn(II): Biofilm formation, community structure, and microbial function. Sci Total Environ 2024; 928:172397. [PMID: 38608889 DOI: 10.1016/j.scitotenv.2024.172397] [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] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/22/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024]
Abstract
Microplastic biofilms are novel vectors for the transport and spread of pathogenic and drug-resistant bacteria. With the increasing use of bio-based plastics, there is an urgent need to investigate the microbial colonization characteristics of these materials in seawater, particularly in comparison with conventional petroleum-based plastics. Furthermore, the effect of co-occurring contaminants, such as heavy metals, on the formation of microplastic biofilms and bacterial communities remains unclear. In this study, we compared the biofilm bacterial community structure of petroleum-based polyethylene (PE) and bio-based polylactic acid (PLA) in seawater under the influence of zinc ions (Zn2+). Our findings indicate that the biofilm on PLA microplastics in the late stage was impeded by the formation of a mildly acidic microenvironment resulting from the hydrolysis of the ester group on PLA. The PE surface had higher bacterial abundance and diversity, with a more intricate symbiotic pattern. The bacterial structures on the two types of microplastics were different; PE was more conducive to the colonization of anaerobic bacteria, whereas PLA was more favorable for the colonization of aerobic and acid-tolerant species. Furthermore, Zn increased the proportion of the dominant genera that could utilize microplastics as a carbon source, such as Alcanivorax and Nitratireductor. PLA had a greater propensity to harbor and disseminate pathogenic and drug-resistant bacteria, and Zn promoted the enrichment and spread of harmful bacteria such as, Pseudomonas and Clostridioides. Therefore, further research is essential to fully understand the potential environmental effects of bio-based microplastics and the role of heavy metals in the dynamics of bacterial colonization.
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Affiliation(s)
- Wang-Chao Chu
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Yuan-Yuan Gao
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Yu-Xin Wu
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Fei-Fei Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China.
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Long GY, Yang XB, Wang Z, Zeng QH, Yang H, Jin DC. Wing expansion functional analysis of ion transport peptide gene in Sogatella furcifera (Horváth) (Hemiptera: Delphacidae). Comp Biochem Physiol B Biochem Mol Biol 2024; 271:110946. [PMID: 38266956 DOI: 10.1016/j.cbpb.2024.110946] [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: 06/13/2023] [Revised: 01/20/2024] [Accepted: 01/20/2024] [Indexed: 01/26/2024]
Abstract
Ion transport peptide (ITP), a superfamily of arthropod neuropeptides, serves a crucial role in regulating various physiological processes such as diuresis, ecdysis behavior, and wing expansion. However, the molecular characteristics, expression profile, and role of ITP in Sogatella furcifera are poorly understood. To elucidate the characteristics and biological function of ITP in S. furcifera, we employed reverse transcription-polymerase chain reaction (RT-PCR) and RNA interference (RNAi) methods. The identified SfITP gene encodes 117 amino acids. The expression of SfITP gradually increased followed the formation of 3-day-old of 5th instar nymph, peaking initially at 40 min after eclosion, and reaching another peak 24 h after eclosion, with particularly high expression levels in thorax and wing tissues. Notably, SfITP RNAi in 3rd instar nymphs of S. furcifera significantly inhibited the transcript levels of SfITP, resulting in 55% mortality and 78% wing deformity. These findings suggests that SfITP is involved in the regulation of wing expansion in S. furcifera, providing insights into the regulation of insect wing expansion and contributing to the molecular understanding of this process.
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Affiliation(s)
- Gui-Yun Long
- School of Chinese Ethnic Medicine, Guizhou Minzu University, Key Laboratory of Guizhou Ethnic Medicine Resource Development and Utilization in Guizhou Minzu University, State Ethnic Affairs Commission, Guiyang 550025, China; Institute of Entomology, Guizhou University, Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions and Scientific Observation and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang 550025, China
| | - Xi-Bin Yang
- Institute of Entomology, Guizhou University, Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions and Scientific Observation and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang 550025, China; Plant Protection and Quarantine Station, Department of Agriculture and Rural Affairs of Guizhou Province, Guiyang 550001, People's Republic of China
| | - Zhao Wang
- College of Environment and Life Sciences, Kaili University, Kaili 556011, China
| | - Qing-Hui Zeng
- Institute of Entomology, Guizhou University, Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions and Scientific Observation and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang 550025, China
| | - Hong Yang
- Institute of Entomology, Guizhou University, Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions and Scientific Observation and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang 550025, China.
| | - Dao-Chao Jin
- Institute of Entomology, Guizhou University, Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions and Scientific Observation and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang 550025, China.
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7
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Ma G, Zhang Y, Li X. Overexpression of OsDUF6 increases salt stress tolerance in rice. BMC Plant Biol 2024; 24:216. [PMID: 38532340 DOI: 10.1186/s12870-024-04921-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024]
Abstract
BACKGROUND Soil salinity is one of the primary environmental stresses faced in rice production. When plants are exposed to salt stress, a series of cellular balances will be disrupted. Dufulin is an immune-induced antiviral agent used in plants. The DUF gene family influences plant response to abiotic stress, and the functional role of OsDUF6(ABA98726.1) in rice response to salt stress is being investigated here. RESULTS Based on the transcriptome analysis of Dufulin treatment in inducing salt tolerance in rice, we selected the OsDUF6 protein located on the cell membrane and studied its molecular function by overexpressing OsDUF6. Salt-induced decreases in root, stem, and leaf length and increased leaf yellowing rate and Na+ concentration in the wild-type plant were mitigated in the overexpressed lines. OsDUF6 overexpression increased the enzymatic antioxidant activities of superoxide dismutase, peroxidase, catalase, and phenylalanine ammonia-lyase. OsDUF6 also played a positive role in Na+ transport as reflected by the increased growth of a salt-sensitive yeast mutant complemented with OsDUF6 in the presence of salt stress. In addition, Reverse transcription quantitative PCR analysis confirmed that the overexpression of OsDUF6 significantly changed the expression level of other genes related to growth and stress tolerance. CONCLUSIONS Combined with previously published data, our results supported the observation that OsDUF6 is an important functional factor in Dufulin-induced promotion of salt stress tolerance in rice.
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Affiliation(s)
- Guangming Ma
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticides and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Yong Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticides and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Xiangyang Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticides and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China.
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Sidorenkov AV, Borokhovski EF. Comparative Analysis of the Functions Work Groups and Informal Subgroups Carry out in Relation to their Members: The Essence, Conditions of Implementation, Effects, and Dysfunctions. Integr Psychol Behav Sci 2024:10.1007/s12124-024-09834-y. [PMID: 38492193 DOI: 10.1007/s12124-024-09834-y] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2024] [Indexed: 03/18/2024]
Abstract
In this article, we attempt to integrate and further develop conceptual ideas about functions of small groups and the informal subgroups that arise within them in relation to their respective members, namely, the functions of: (1) creating possibilities for realizing individual goals and meeting individual needs; (2) providing protection from external and intragroup social threats; (3) providing information to members; (4) educating members; (5) providing adaptive capacities to members; and (6) providing control and regulation. First, drawing on a functional analysis, we defined the concept of "function." Next, we touched upon such issues as: the essence of each function; conditions for implementing the functions; the difference between an informal subgroup and a small group in how they implement the functions for their respective members; the effects of implementing the functions; and the related dysfunctions. This versatile account of the functions that small groups and informal subgroups implement in relation to their members allowed us to expand our understanding of these functions and their effects on attitudes, activities and the development of group (subgroup) members, as well as of some aspects of group and subgroup processes and performance. We conclude by presenting both theoretical and practical applications of the analysis of the functions of groups and subgroups and, accordingly, posed some important questions for further research and discussion.
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Affiliation(s)
- Andrey V Sidorenkov
- Southern Federal University, 105/42 Bolshaya Sadovaya Ul., Rostov-Na-Donu, 344006, Russia
| | - Eugene F Borokhovski
- Concordia University, Boulevard de Maisonneuve West, 1455, H3G 1M8, Montreal, QC, GA‑2.126, Canada.
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Naim D, Ahsan A, Imtiaj A, Mollah NH. Genome-wide identification and in silico characterization of major RNAi gene families in date palm (Phoenix dactylifera). BMC Genom Data 2024; 25:31. [PMID: 38491426 PMCID: PMC10943882 DOI: 10.1186/s12863-024-01217-x] [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: 05/13/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Dates contain various minerals that are essential for good health. The major RNA interference (RNAi) gene families play a vital role in plant growth and development by controlling the expression of protein-coding genes against different biotic and abiotic stresses. However, these gene families for date palm are not yet studied. Therefore, this study has explored major RNAi genes and their characteristics in date palm. RESULTS We have identified 4 PdDCLs, 7 PdAGOs, and 3 PdRDRs as RNAi proteins from the date palm genome by using AtRNAi genes as query sequences in BLASTp search. Domain analysis of predicted RNAi genes has revealed the Helicase_C, Dicer_dimer, PAZ, RNase III, and Piwi domains that are associated with the gene silencing mechanisms. Most PdRNAi proteins have been found in the nucleus and cytosol associated with the gene silencing actions. The gene ontology (GO) enrichment analysis has revealed some important GO terms including RNA interference, dsRNA fragmentation, and ribonuclease_III activity that are related to the protein-coding gene silencing mechanisms. Gene regulatory network (GRN) analysis has identified PAZ and SNF2 as the transcriptional regulators of PdRNAi genes. Top-ranked 10 microRNAs including Pda-miR156b, Pda-miR396a, Pda-miR166a, Pda-miR167d, and Pda-miR529a have been identified as the key post-transcriptional regulators of PdRNAi genes that are associated with different biotic/abiotic stresses. The cis-acting regulatory element analysis of PdRNAi genes has detected some vital cis-acting elements including ABRE, MBS, MYB, MYC, Box-4, G-box, I-box, and STRE that are linked with different abiotic stresses. CONCLUSION The results of this study might be valuable resources for the improvement of different characteristics in date palm by further studies in wet-lab.
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Affiliation(s)
- Darun Naim
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Asif Ahsan
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Ahmed Imtiaj
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh.
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Dumas T, Martinez Pinna R, Lozano C, Radau S, Pible O, Grenga L, Armengaud J. The astounding exhaustiveness and speed of the Astral mass analyzer for highly complex samples is a quantum leap in the functional analysis of microbiomes. Microbiome 2024; 12:46. [PMID: 38454512 PMCID: PMC10918999 DOI: 10.1186/s40168-024-01766-4] [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] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/17/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND By analyzing the proteins which are the workhorses of biological systems, metaproteomics allows us to list the taxa present in any microbiota, monitor their relative biomass, and characterize the functioning of complex biological systems. RESULTS Here, we present a new strategy for rapidly determining the microbial community structure of a given sample and designing a customized protein sequence database to optimally exploit extensive tandem mass spectrometry data. This approach leverages the capabilities of the first generation of Quadrupole Orbitrap mass spectrometer incorporating an asymmetric track lossless (Astral) analyzer, offering rapid MS/MS scan speed and sensitivity. We took advantage of data-dependent acquisition and data-independent acquisition strategies using a peptide extract from a human fecal sample spiked with precise amounts of peptides from two reference bacteria. CONCLUSIONS Our approach, which combines both acquisition methods, proves to be time-efficient while processing extensive generic databases and massive datasets, achieving a coverage of more than 122,000 unique peptides and 38,000 protein groups within a 30-min DIA run. This marks a significant departure from current state-of-the-art metaproteomics methodologies, resulting in broader coverage of the metabolic pathways governing the biological system. In combination, our strategy and the Astral mass analyzer represent a quantum leap in the functional analysis of microbiomes. Video Abstract.
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Affiliation(s)
- Thibaut Dumas
- Département Médicaments Et Technologies Pour La Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200, Bagnols-Sur-Cèze, France
| | | | - Clément Lozano
- Département Médicaments Et Technologies Pour La Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200, Bagnols-Sur-Cèze, France
| | - Sonja Radau
- Thermo Fisher Scientific GmbH, 63303, Dreieich, Germany
| | - Olivier Pible
- Département Médicaments Et Technologies Pour La Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200, Bagnols-Sur-Cèze, France
| | - Lucia Grenga
- Département Médicaments Et Technologies Pour La Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200, Bagnols-Sur-Cèze, France
| | - Jean Armengaud
- Département Médicaments Et Technologies Pour La Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200, Bagnols-Sur-Cèze, France.
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11
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Hallam R, Brown G, Turner L, Blomfield E, El Leithy S, Mendes I. Development of a training programme in individual case formulation skills and a scale for assessing its effectiveness. Behav Cogn Psychother 2024; 52:200-203. [PMID: 37994482 DOI: 10.1017/s1352465823000577] [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] [Indexed: 11/24/2023]
Abstract
BACKGROUND Little is known about the skills involved in clinical formulation. The individual case formulation (ICF) approach, based on functional analysis, employs clinical descriptions that are theory-free and depicts formulations constructed according to a set of basic conventions. AIMS We report a test of whether this method could be taught and if the quality of the resulting diagrams could be reliably rated. METHOD Participants (n=40) participated in a training course in formulation. A draft rating scale was refined in the course of rating formulation diagrams and basic inter-rater reliability established. RESULTS Results of the study support further development of the ICF approach.
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Affiliation(s)
| | - Gary Brown
- Royal Holloway University of London, London, UK
| | - Liza Turner
- Royal Holloway University of London, London, UK
| | | | | | - Ines Mendes
- Royal Holloway University of London, London, UK
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Wu J, Zhang J, Hao X, Lv K, Xie Y, Xu W. Establishment of an efficient callus transient transformation system for Vitis vinifera cv. 'Chardonnay'. Protoplasma 2024; 261:351-366. [PMID: 37906315 DOI: 10.1007/s00709-023-01901-2] [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: 03/30/2023] [Accepted: 10/09/2023] [Indexed: 11/02/2023]
Abstract
Grape (Vitis L.), a highly valued fruit crop, poses significant challenges in genetic transformation and functional characterization of genes. Therefore, there is an urgent need for the development of a rapid and effective method for grape transformation and gene function identification. Here, we introduce a streamlined Agrobacterium-mediated transient transformation system for grape calli. Optimal conditions were established with a leaf-derived callus induction medium; chiefly B5 medium supplemented with 0.05 mg/L NAA, 0.5 mg/L 2,4-D, and 2.0 mg/L KT; and a callus proliferation medium (B5 medium supplemented with 0.5 mg/L NAA and 2.0 mg/L 6-BA), respectively. Notably, GUS enzyme activity peaked (352.96 ± 33.95 mol 4-MU/mg/min) by sonication with Agrobacterium tumefaciens EHA105 and 100 μM AS for 4 min, followed by vacuum infection for 5 min, and co-culture at 25 °C in the dark for 1 day using callus as explants at an optical density (OD600) of 0.8. VaCIPK18 gene was transiently transformed into calli, and transcripts of the gene (endogenous and exogenous) were detected at higher levels than in non-transformed calli (endogenous). Moreover, after 10 days of treatment at 4 °C or -4 °C, the callus net weight of transformed callus was significantly higher than that of the untransformed callus, indicating that the VaCIPK18-overexpressing grape callus could improve cold tolerance. Overall, we establish a simple but effective transient transformation approach for grape callus, which could serve as a useful tool for the rapid assessment of gene function in this important crop.
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Affiliation(s)
- Jieping Wu
- College of Enology and Horticulture, Ningxia University, Yinchuan, 750021, Ningxia, China
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan, 750021, Ningxia, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, 750021, China
| | - Junxia Zhang
- College of Enology and Horticulture, Ningxia University, Yinchuan, 750021, Ningxia, China
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan, 750021, Ningxia, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, 750021, China
| | - Xinyi Hao
- College of Enology and Horticulture, Ningxia University, Yinchuan, 750021, Ningxia, China
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan, 750021, Ningxia, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, 750021, China
| | - Kai Lv
- College of Enology and Horticulture, Ningxia University, Yinchuan, 750021, Ningxia, China
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan, 750021, Ningxia, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, 750021, China
| | - Yaping Xie
- College of Enology and Horticulture, Ningxia University, Yinchuan, 750021, Ningxia, China
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan, 750021, Ningxia, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, 750021, China
| | - Weirong Xu
- College of Enology and Horticulture, Ningxia University, Yinchuan, 750021, Ningxia, China.
- Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan, 750021, Ningxia, China.
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, 750021, China.
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Zhu J, Li Y, Zhang Y, Xia L, Hu W, Huang X, Li K, He X, Luo C. Overexpression of MiSPL3a and MiSPL3b confers early flowering and stress tolerance in Arabidopsis thaliana. Int J Biol Macromol 2024; 262:129913. [PMID: 38336312 DOI: 10.1016/j.ijbiomac.2024.129913] [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: 11/01/2023] [Revised: 01/11/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
Abstract
SQUAMOSA promoter-binding protein-like (SPL) family genes play an important role in regulating plant flowering and resistance to stress. However, understanding the function of the SPL family in mango is still limited. In a previous study, two MiSPL3 genes, MiSPL3a and MiSPL3b (MiSPL3a/b), were identified in 'SiJiMi' mango and exhibited the highest expression in flowers at the initial flowering stage [24]. Therefore, in this study, we further investigated the expression pattern and gene function of MiSPL3a/b. The results showed that the expression of MiSPL3a was greatest at the end of floral bud differentiation, and MiSPL3b was expressed mainly during the flowering induction and vegetative growth stages. Subcellular localization showed that MiSPL3a/b localized to the nucleus. In addition, ectopic expression of MiSPL3a/b promoted earlier flowering in Arabidopsis thaliana by 3 d-6 d than in wild-type (WT) plants, which increased the expression of SUPPRESSOR OF CONSTANS1 (AtSOC1), FRUITFULL (AtFUL), and APETALA1 (AtAP1). MiSPL3a/b transgenic lines exhibited increased tolerance to drought, GA3, and abscisic acid (ABA) treatments but were sensitive to Pro-Ca treatment. Furthermore, protein interaction analysis revealed that MiSPL3a/b could interact with several stress-related proteins, flowering-related proteins, and the bridge protein 14-3-3. Taken together, MiSPL3a and MiSPL3b acted as positive regulators of flowering time and stress tolerance in transgenic Arabidopsis.
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Affiliation(s)
- Jiawei Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China; College of Horticulture, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yuze Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Yili Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - LiMing Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Wanli Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Xing Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Kaijiang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
| | - Xinhua He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China.
| | - Cong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China.
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Anu K, Kumari S, Choudhary G, Devi S. Microbial diversity analysis of Chumathang geothermal spring, Ladakh, India. Braz J Microbiol 2024:10.1007/s42770-024-01284-3. [PMID: 38421596 DOI: 10.1007/s42770-024-01284-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
In light of their unique and challenging environment, the high-altitude Chumathang geothermal springs in Ladakh, India, are undeniably intriguing for microbiological study. The purpose of this study was to employ a culture-independent sequencing approach to give a comprehensive characterization of the unknown bacterial and archaeal community structure, composition and networks in water and soil from the Chumathang geothermal spring. A total of 50%, and 42.86% bacterial phyla were found in the water, and soil samples respectively and this analysis also showed a total of 9.62% and 7.94% of archaeal phyla in both the samples, respectively. Further, the presence of unclassified (derived from other sequences, water: 17.31%, and soil: 19.05%) and unclassified (derived from bacteria, water: 13.46%, and soil: 12.70%) were also observed in the current metagenomics investigation. Firmicutes and Proteobacteria were the most abundant bacterial phyla in water, whereas Proteobacteria and Bacteroidetes were the most abundant bacterial phyla in geothermal soil. Crenarchaeota and Euryarchaeota dominated archeal communities in soil and water, respectively. This metagenomic study gave a detailed insight into the microbial diversity found in Chumathang geothermal spring and surrounding area, located in Ladakh, India. Surprisingly, this finding indicated the existence of geographically distinct microbial communities that were suited to various geothermal water habitats along the Himalayan Geothermal Belt. Future studies must take into account the metabolic pathways of these microbial communities that exist in these extreme environments. This will allow us to obtain a better knowledge of the microbial metabolisms that are common at these geothermal locations, which have a lot of potential for biotechnological applications. They will also enable us to establish links between the microbial community composition and the physicochemical environment of geothermal water and area.
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Affiliation(s)
- Kumari Anu
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shalini Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Geetanjli Choudhary
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Sarita Devi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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15
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Cai X, Li K, Meng X, Song Q, Shi S, Li W, Niu Y, Jin L, Kan H, Wang S. Epigenome-wide association study on short-, intermediate- and long-term ozone exposure in Han Chinese, the NSPT study. J Hazard Mater 2024; 463:132780. [PMID: 37898092 DOI: 10.1016/j.jhazmat.2023.132780] [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: 06/09/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023]
Abstract
Epidemiological and epigenetic studies have acknowledged ambient ozone exposure associated with inflammatory and cardiovascular disease. However, the molecular mechanisms still remained unclear, and epigenome-wide analysis in cohort were lacking, especially in Chinese. We included blood-derived DNA methylation for 3365 Chinese participants from the NSPT cohort and estimated individual ozone exposure level of short-, intermediate- and long-term, based on a validated prediction model. We performed epigenome-wide association studies which identified 59 CpGs and 30 DMRs at a strict genome-wide significance (P < 5 ×10-8). We also conducted comparison on the DNA methylation alteration corresponding to different time windows, and observed an enhanced differentiated methylation trend for intermediate- and long-term exposure, while the short-term exposure associated methylation changes did not retain. The targeted genes of methylation alteration were involved in mechanism related to aging, inflammation disease, metabolic syndrome, neurodevelopmental disorders, and oncogenesis. Underlying pathways were enriched in biological activities including telomere maintenance process, DNA damage response and megakaryocyte differentiation. In conclusion, our study is the first EWAS on ozone exposure conducted in large-scale Han Chinese cohort and identified associated DNA methylation change on CpGs and regions, as well as related gene functions and pathways.
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Affiliation(s)
- Xiyang Cai
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kaixuan Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xia Meng
- School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai 200032, China
| | - Qinglin Song
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Su Shi
- School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai 200032, China
| | - Wenran Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yue Niu
- School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai 200032, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, and Human Phenome Institute, Fudan University, Shanghai, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China; Taizhou Institute of Health Sciences, Fudan University, Taizhou, Jiangsu, China
| | - Haidong Kan
- School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai 200032, China; Children's Hospital of Fudan University, National Center for Children's Health, Shanghai 201102, China.
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China; Taizhou Institute of Health Sciences, Fudan University, Taizhou, Jiangsu, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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16
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Aktar N, Mannan E, Kabir SMT, Hasan R, Hossain MS, Ahmed R, Ahmed B, Islam MS. Comparative metagenomics and microbial dynamics of jute retting environment. Int Microbiol 2024; 27:113-126. [PMID: 37204507 DOI: 10.1007/s10123-023-00377-7] [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: 01/23/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023]
Abstract
Jute, eco-friendly natural fiber, depends on conventional water-based microbial retting process that suffers from the production of low-quality fiber, restricting its diversified applications. The efficiency of water retting of jute depends on plant polysaccharide fermenting pectinolytic microorganisms. Understanding the phase difference in retting microbial community composition is crucial to provide knowledge on the functions of each member of microbiota for the improvement of retting and fiber quality. The retting microbiota profiling of jute was commonly performed previously using only one retting phase with culture-dependent methods which has limited coverage and accuracy. Here, for the first we have analyzed jute retting water through WGS metagenome approach in three phases (pre-retting, aerobic retting, and anaerobic retting phases) and characterized the microbial communities both culturable and non-culturable along with their dynamics with the fluctuation of oxygen availability. Our analysis revealed a total of 25.99 × 104 unknown proteins (13.75%), 16.18 × 105 annotated proteins (86.08%), and 32.68 × 102 ribosomal RNA (0.17%) in the pre-retting phase, 15.12 × 104 unknown proteins (8.53%), 16.18 × 105 annotated proteins (91.25%), and 38.62 × 102 ribosomal RNA (0.22%) in the aerobic retting phase, and 22.68 × 102 ribosomal RNA and 80.14 × 104 (99.72%) annotated protein in the anaerobic retting phase. Taxonomically, we identified 53 different phylotypes in the retting environment, with Proteobacteria being the dominant taxa comprising over 60% of the population. We have identified 915 genera from Archaea, Viruses, Bacteria, and Eukaryota in the retting habitat, with anaerobic or facultative anaerobic pectinolytic microflora being enriched in the anoxic, nutrient-rich retting niche, such as Aeromonas (7%), Bacteroides (3%), Clostridium (6%), Desulfovibrio (4%), Acinetobacter (4%), Enterobacter (1%), Prevotella (2%), Acidovorax (3%), Bacillus (1%), Burkholderia (1%), Dechloromonas (2%), Caulobacter (1%) and Pseudomonas (7%). We observed an increase in the expression of 30 different KO functional level 3 pathways in the final retting stage compared to the middle and pre-retting stages. The main functional differences among the retting phases were found to be related to nutrient absorption and bacterial colonization. These findings reveal the bacterial groups that are involved in fiber retting different phases and will facilitate to develop future phase-specific microbial consortia for the improvement of jute retting process.
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Affiliation(s)
- Nasima Aktar
- Basic and Applied Research on Jute, Dhaka, Bangladesh.
| | | | | | - Rajnee Hasan
- Basic and Applied Research on Jute, Dhaka, Bangladesh
| | - Md Sabbir Hossain
- Basic and Applied Research on Jute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Rasel Ahmed
- Basic and Applied Research on Jute, Dhaka, Bangladesh
| | - Borhan Ahmed
- Basic and Applied Research on Jute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Md Shahidul Islam
- Basic and Applied Research on Jute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
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Hernández-Preciado MR, Torres-Mendoza BM, Mireles-Ramírez MA, Kobayashi-Gutiérrez A, Sánchez-Rosales NA, Vázquez-Valls E, Marquez-Pedroza J. Gene expression in multiple sclerosis during pregnancy based on integrated bioinformatics analysis. Mult Scler Relat Disord 2024; 82:105373. [PMID: 38154347 DOI: 10.1016/j.msard.2023.105373] [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: 08/22/2023] [Revised: 11/17/2023] [Accepted: 12/10/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND The modulation of the activity disease in patients with Multiple Sclerosis (MS) that occurs during pregnancy is a helpful model which could provide insight into central disease mechanisms and facilitate treatment. Therefore, the aim of the study was to identify differentially expressed genes in-silico to perform biological function pathway enrichment analysis and protein-protein interaction from pregnant women with MS. METHODS Transcriptome data were obtained from the Gene Expression Omnibus (GEO) database. We selected the microarray dataset GSE17449. The gene expression dataset contains the data of mononuclear cells from four different groups sought, including seven healthy women (H), four healthy pregnant women (HP), eight women with multiple sclerosis (WMS), and nine women nine months pregnant with multiple sclerosis (PMS). The GSEA software was employed for enrichment analysis, and the REACTOME database was used for biological pathways. The protein-protein interaction (PPI) network was plotted with STRING. The databases used to identify the connection of DEGs with different signaling pathways were KEGG and WIKIPATHWAYS. RESULTS We identified 42 differentially expressed genes in pregnant women with MS. The significant pathways included IL-10 signaling pathway, ErbB2 activates, the hemoglobin complex (HBD, HBB, HBA1, AHSP, and HBA2), IL-17 signaling pathway (LCN2 and MMP9), antigen processing and presentation, and Th17 cell differentiation (HLA-DQA1), Rap1 signaling pathway (ID1), NOD-Like receptor signaling pathway (CAMP and DEFA4), PD-L1 Signaling, Interferon gamma signaling (MMP9 and ARG1), Neutrophil degranulation (CAMP, DEFA4, ELANE, CEACAM8, S100P, CHI3L1, AZU1, OLFM4, CRISP3, LTF, ARG1, PGLYRP1, and TCN1). In the WIKIPATHWAYS set, significance was found Vitamin B12 metabolism (TCN1, HBB, and HBA2), and IL-18 signaling pathway (S100P). CONCLUSION This study can be used to understand several essential target genes and pathways identified in the present study, which may serve as feasible targets for MS therapies.
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Affiliation(s)
- Martha Rocio Hernández-Preciado
- High Specialty Medical Unit, Pediatric Hospital, Western National Medical Center of the Mexican Institute of Social Security, Guadalajara 44340, Mexico; Department of Philosophical and Methodological Disciplines, University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Mexico
| | - Blanca Miriam Torres-Mendoza
- Department of Philosophical and Methodological Disciplines, University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Mexico; Neurosciences Division, Western Biomedical Research Center (IMSS), Guadalajara 44340, Mexico
| | - Mario Alberto Mireles-Ramírez
- High Specialty Medical Unit, Western National Medical Center of the Mexican Institute of Social Security, Guadalajara 44340, Mexico
| | - Antonio Kobayashi-Gutiérrez
- High Specialty Medical Unit, Western National Medical Center of the Mexican Institute of Social Security, Guadalajara 44340, Mexico; PhD in Psychology of Health, University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Mexico
| | - Nayeli Alejandra Sánchez-Rosales
- High Specialty Medical Unit, Western National Medical Center of the Mexican Institute of Social Security, Guadalajara 44340, Mexico
| | - Eduardo Vázquez-Valls
- Directorate of Generation of Professional Resources, Research, and Development, Secretary of Health, Guadalajara 44100, Mexico
| | - Jazmin Marquez-Pedroza
- Neurosciences Division, Western Biomedical Research Center (IMSS), Guadalajara 44340, Mexico.
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Hu Q, Hu Z, Yan X, Lu J, Wang C. Extracellular vesicles involved in growth regulation and metabolic modulation in Haematococcus pluvialis. Biotechnol Biofuels Bioprod 2024; 17:15. [PMID: 38282041 PMCID: PMC10823724 DOI: 10.1186/s13068-024-02462-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/12/2024] [Indexed: 01/30/2024]
Abstract
BACKGROUND Microalgae-derived extracellular vesicles (EVs), which transfer their cargos to the extracellular environment to affect recipient cells, play important roles in microalgal growth and environmental adaptation. And, they are also considered as sustainable and renewable bioresources of delivery nanocarrier for bioactive molecules and/or artificial drug molecules. However, their molecular composition and functions remain poorly understood. RESULTS In this study, isolation, characterization, and functional verification of Haematococcus pluvialis-derived EVs (HpEVs) were performed. The results indicated that HpEVs with typical EV morphology and size were secreted by H. pluvialis cells during the whole period of growth and accumulated in the culture medium. Cellular uptake of HpEVs by H. pluvialis was confirmed, and their roles in regulation of growth and various physiological processes of the recipient cells were also characterized. The short-term inhibition of HpEV secretion results in the accumulation of functional cellular components of HpEVs, thereby altering the biological response of these cells at the molecular level. Meanwhile, continuously inhibiting the secretion of HpEVs negatively influenced growth, and fatty acid and astaxanthin accumulation in H. pluvialis. Small RNA high-throughput sequencing was further performed to determine the miRNA cargoes and compelling details in HpEVs in depth. Comparative analysis revealed commonalities and differences in miRNA species and expression levels in three stages of HpEVs. A total of 163 mature miRNAs were identified with a few unique miRNAs reveal the highest expression levels, and miRNA expression profile of the HpEVs exhibited a clear stage-specific pattern. Moreover, a total of 12 differentially expressed miRNAs were identified and their target genes were classified to cell cycle control, lipid transport and metabolism, secondary metabolites biosynthesis and so on. CONCLUSION It was therefore proposed that cargos of HpEVs, including miRNA constituents, were suggested potential roles in modulate cell physiological state of H. pluvialis. To summarize, this work uncovers the intercellular communication and metabolism regulation functions of HpEVs.
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Affiliation(s)
- Qunju Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Zhangli Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Xiaojun Yan
- College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Jun Lu
- Auckland Bioengineering Institute, University of Auckland, Auckland, 1142, New Zealand
| | - Chaogang Wang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
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19
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Zhang P, Liu D, Ma J, Sun C, Wang Z, Zhu Y, Zhang X, Liu Y. Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe. BMC Genomics 2024; 25:83. [PMID: 38245685 PMCID: PMC10799369 DOI: 10.1186/s12864-024-09966-w] [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: 11/19/2023] [Accepted: 01/03/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Protein phosphatases type 2C (PP2C) are heavily involved in plant growth and development, hormone-related signaling pathways and the response of various biotic and abiotic stresses. However, a comprehensive report identifying the genome-scale of PP2C gene family in ginger is yet to be published. RESULTS In this study, 97 ZoPP2C genes were identified based on the ginger genome. These genes were classified into 15 branches (A-O) according to the phylogenetic analysis and distributed unevenly on 11 ginger chromosomes. The proteins mainly functioned in the nucleus. Similar motif patterns and exon/intron arrangement structures were identified in the same subfamily of ZoPP2Cs. Collinearity analysis indicated that ZoPP2Cs had 33 pairs of fragment duplicated events uniformly distributed on the corresponding chromosomes. Furthermore, ZoPP2Cs showed greater evolutionary proximity to banana's PP2Cs. The forecast of cis-regulatory elements and transcription factor binding sites demonstrated that ZoPP2Cs participate in ginger growth, development, and responses to hormones and stresses. ZoERFs have plenty of binding sites of ZoPP2Cs, suggesting a potential synergistic contribution between ZoERFs and ZoPP2Cs towards regulating growth/development and adverse conditions. The protein-protein interaction network displayed that five ZoPP2Cs (9/23/26/49/92) proteins have robust interaction relationship and potential function as hub proteins. Furthermore, the RNA-Seq and qRT-PCR analyses have shown that ZoPP2Cs exhibit various expression patterns during ginger maturation and responses to environmental stresses such as chilling, drought, flooding, salt, and Fusarium solani. Notably, exogenous application of melatonin led to notable up-regulation of ZoPP2Cs (17/59/11/72/43) under chilling stress. CONCLUSIONS Taken together, our investigation provides significant insights of the ginger PP2C gene family and establishes the groundwork for its functional validation and genetic engineering applications.
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Affiliation(s)
- Pan Zhang
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Deqi Liu
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Jiawei Ma
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Chong Sun
- Special Plants Institute, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Zhaofei Wang
- Special Plants Institute, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Yongxing Zhu
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Xuemei Zhang
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Yiqing Liu
- College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze University, Jingzhou, 434025, Hubei, China.
- Special Plants Institute, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China.
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Wang M, Hong L, Cai L, Zhang Z, Jiang N, Chen Y, Ying Q, Kong L, Wei Z, Xu Y, Jin L. Novel LDLR variants affecting low density lipoprotein metabolism identified in familial hypercholesterolemia. Mol Biol Rep 2024; 51:153. [PMID: 38236436 DOI: 10.1007/s11033-023-09169-8] [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: 10/12/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND Familial hypercholesterolemia (FH) is an autosomal dominant disease of lipid metabolism mainly caused by mutations in the low-density lipoprotein receptor (LDLR) gene. Genetic detection of patients with FH help with precise diagnosis and treatment, thus reducing the risk of coronary heart disease (CHD) and other related diseases. The study aimed to identify the causative gene mutations in a Chinese FH family and reveal the pathogenicity and the mechanism of these mutations. METHODS AND RESULTS Whole exome sequencing was performed in a patient with severe lipid metabolism dysfunction seeking fertility guidance from a Chinese FH family. Two LDLR variants c.1875 C > G (p.N625K; novel variant) and c.1448G > A (p.W483*) were identified in the family. Wildtype and mutant LDLR constructs were established by the site-direct mutagenesis technique. Functional studies were carried out by cell transfection to evaluate the impact of detected variants on LDLR activity. The two variants were proven to affect LDL uptake and binding, resulting in cholesterol clearance reduction to different degrees. According to The American College of Medical Genetics and Genomics (ACMG) Standards and Guidelines, the W483* variant was classified as "Pathogenic", while the N625K variant as "VUS". CONCLUSIONS Our results provide novel experimental evidence of functional alteration by LDLR variants identified in our study and expand the mutational spectrum of LDLR mutation induced FH.
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Affiliation(s)
- Miao Wang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Ling Hong
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Luyi Cai
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Ziyi Zhang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Ningdong Jiang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yijing Chen
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Qian Ying
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Lingpeng Kong
- Department of Computer Science, The University of Hong Kong, Hong Kong, China
| | - Zhiyun Wei
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
| | - Yao Xu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
| | - Liping Jin
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
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Shu M, Xu H, Liang Y, Shi M, Chen M, Guo J. Long Non-Coding RNA BCYRN1 Drives Cellular Processes to Promote Asthma Development. Int Arch Allergy Immunol 2024; 185:343-354. [PMID: 38224673 DOI: 10.1159/000535868] [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: 11/24/2023] [Accepted: 12/14/2023] [Indexed: 01/17/2024] Open
Abstract
INTRODUCTION Asthma is a common chronic inflammatory respiratory disease worldwide. The long non-coding RNA (lncRNA) BCYRN1 has been shown to function in the inhibition of smooth muscle cell differentiation and vascular development, but its function and potential molecular mechanisms of lncRNA BCYRN1 in bronchial smooth muscle cells (BSMCs) in asthma remain unknown. METHODS Quantitative real-time polymerase chain reaction (RT-qPCR) was performed to detect the expression level of lncRNA BCYRN1 in blood and sputum of asthma patients. The effects of lncRNA BCYRN1 on the proliferation and migration of BSMCs were explored by cell counting kit-8, Transwell, colony formation, and flow cytometry analysis. Differentially expressed genes between lncRNA BCYRN1 overexpression and knockdown cells were identified using RNA-seq and verified using RT-qPCR. RESULTS LncRNA BCYRN1 was upregulated in asthma patients. Overexpression of lncRNA BCYRN1 significantly promoted the proliferation and migration of BSMCs, inhibited cell apoptosis and affected cell cycle arrest, promoting DNA replication. These effects were reversed after lncRNA BCYRN1 inhibition. RNA-seq identified 434 common differentially expressed genes in the lncRNA BCYRN1 overexpression and knockdown groups and verified their expression levels by RT-qPCR. Gene ontology, Kyoto Encyclopedia of Genes and Genomes and Gene set enrichment analysis indicated that these genes were mainly involved in external stimulus, cell cycle, growth factor activity, cytokine interactions, and inflammatory response. CONCLUSION The identification of the highly expressed lncRNA BCYRN1 in patients with asthma, combined with functional experiments and transcriptional data, suggests that lncRNA BCYRN1 can mediate the development of asthma and can be used as a promising diagnostic and prognostic biomarker for asthma.
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Affiliation(s)
- Min Shu
- Department of Emergency, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Hongbo Xu
- Department of Emergency, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Yongsheng Liang
- Department of Emergency, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Mengjuan Shi
- Department of Emergency, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Ming Chen
- Department of Emergency, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Jianghua Guo
- Department of Emergency, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
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Zhao M, Gao Z, Ji X, Wang K, Zhang S, Shi Y, Song X, Yu Z, Yang X. The diverse functions of Mu-class Glutathione S-transferase HrGSTm1 during the development of Hyalomma rufipes with a focus on the detoxification metabolism of cyhalothrin. Parasit Vectors 2024; 17:1. [PMID: 38167098 PMCID: PMC10759735 DOI: 10.1186/s13071-023-06084-6] [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: 09/14/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Glutathione S-transferases (GSTs) are a superfamily of multifunctional enzymes in living organisms with metabolic and detoxification functions, which can detoxify exogenous and endogenous compounds and thereby reduce the damage caused by toxic substances to the body. Ticks are obligate blood-sucking ectoparasites that can transmit various pathogens, and the characterization of tick-derived GSTs may help improve current understanding of the molecular mechanism of tick resistance to insecticides. In this study, a novel GST gene, named HrGSTm1, was identified from Hyalomma rufipes. METHODS Sequence analysis was performed by using bioinformatics techniques. A prokaryotic expression system was used to obtain the recombinant expression protein rHrGSTm1. Detection of spatiotemporal expression patterns of target genes and their response to the toxicity of cyhalothrin on female H. rufipes was performed by using a quantitative PCR platform. The optimal enzymological parameters of rHrGSTm1 using glutathione as substrate were calculated. The antioxidant capacity of the recombinant protein was evaluated by DPPH• (1,1-Diphenyl-2-picrylhydrazyl radical 2,2-Diphenyl-1-(2,4,6-trinitrophenyl) hydrazyl). Knockdown of the HrGSTm1 genes through RNA interference was used to analyze their effects on the physiological parameters of ticks. The changes in HrGSTm1 messenger RNA expression patterns under cypermethrin stress were analyzed. RESULTS The complementary DNA sequence of HrGSTm1 contained a 672-bp open reading frame, which potentially encoded 223 amino acids. The predicted molecular weight was 25.62 kDa, and the isoelectric point 8.22. HrGSTm1 is a Mu-class GST, belonging to the cytoplasmic GSTs with no signal peptide observed. The Vmax and Km of rHrGSTm1 were 3.367 ± 0.81 uM and 2.208 ± 0.76 uM, respectively, and its activities were dependent on different temperatures and pH conditions; the scavenging rate of rHrGSTm1 to DPPH• reached 76.4% at 1.25 mg/ml. Variable expressions of HrGSTm1 were observed under various treatment periods and in different tissues, with the highest appearing in eggs (analysis of variance [ANOVA], F(2, 9) = 279.9, P < 0.0001) and Malpighian tubules (ANOVA, F(3, 12) = 290.5, P < 0.0001). After knockdown of HrGSTm1, compared with the control group, the mortality in the treatment group was increased by 16.7%, the average oviposition rate decreased by 33.9%, the average engorged body weight decreased by 287.38 mg and egg weight decreased by 127.46 mg, although only the engorged body weight was significantly different (t-test, t(44) = 2.886, P = 0.006). After exposure to three sublethal concentrations (LC05, LC10, LC50) of cyhalothrin, the expression level of HrGSTm1 in the midgut, ovary and salivary gland was upregulated, whereas in Malpighian tubules, it showed a trend of upregulation at first and then downregulation, implying different functions during the detoxification in different tissues. CONCLUSIONS In this study, a novel GST of the Mu-class was successfully isolated from H. rufipes and systematically subjected to bioinformatic analysis and recombination identification. The variation trend of HrGSTm1 expression level in different tissues suggests that the gene has different detoxification functions in different tissues. The potential function of this gene was analyzed to provide basic research for further investigation of its detoxification mechanism.
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Affiliation(s)
- Meichen Zhao
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Zhihua Gao
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Xin Ji
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Kuang Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Songbo Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Yanqing Shi
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Xuecheng Song
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China.
| | - Xiaolong Yang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China.
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Li XZ, Zhang XT, Bie XM, Zhang J, Jiang DJ, Tang H, Wang F. Transcriptome analysis of axillary buds in low phosphorus stress and functional analysis of TaWRKY74s in wheat. BMC Plant Biol 2024; 24:1. [PMID: 38163871 PMCID: PMC10759677 DOI: 10.1186/s12870-023-04695-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 07/25/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Wheat is one of the main grain crops in the world, and the tiller number is a key factor affecting the yield of wheat. Phosphorus is an essential element for tiller development in wheat. However, due to decreasing phosphorus content in soil, there has been increasing use of phosphorus fertilizer, while imposing risk of soil and water pollution. Hence, it is important to identify low phosphorus tolerance genes and utilize them for stress resistance breeding in wheat. RESULTS We subjected the wheat variety Kenong 199 (KN199) to low phosphorus stress and observed a reduced tiller number. Using transcriptome analysis, we identified 1651 upregulated genes and 827 downregulated of genes after low phosphorus stress. The differentially expressed genes were found to be enriched in the enzyme activity regulation related to phosphorus, hormone signal transduction, and ion transmembrane transport. Furthermore, the transcription factor analysis revealed that TaWRKY74s were important for low phosphorus tolerance. TaWRKY74s have three alleles: TaWRKY74-A, TaWRKY74-B, and TaWRKY74-D, and they all belong to the WRKY family with conserved WRKYGQK motifs. These proteins were found to be located in the nucleus, and they were expressed in axillary meristem, shoot apical meristem(SAM), young leaves, leaf primordium, and spikelet primordium. The evolutionary tree showed that TaWRKY74s were closely related to OsWRKY74s in rice. Moreover, TaWRKY74s-RNAi transgenic plants displayed significantly fewer tillers compared to wild-type plants under normal conditions. Additionally, the tiller numebr of the RNAi transgenic plants was also significantly lower than that of the wild-type plants under low-phosphorus stress, and increased the decrease amplitude. This suggestd that TaWRKY74s are related to phosphorus response and can affect the tiller number of wheat. CONCLUSIONS The results of this research showed that TaWRKY74s were key genes in wheat response to low phosphorus stress, which might regulate wheat tiller number through abscisic acid (ABA) and auxin signal transduction pathways. This research lays the foundation for further investigating the mechanism of TaWRKY74s in the low phosphorus environments and is significant for wheat stress resistance breeding.
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Affiliation(s)
- Xue-Zheng Li
- National Key Laboratory of Wheat Breeding, Shandong Agricultural University, Taian, Shandong, 271018, China
- College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Xiao-Tong Zhang
- National Key Laboratory of Wheat Breeding, Shandong Agricultural University, Taian, Shandong, 271018, China
- College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Xiao-Min Bie
- National Key Laboratory of Wheat Breeding, Shandong Agricultural University, Taian, Shandong, 271018, China
- College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Jing Zhang
- National Key Laboratory of Wheat Breeding, Shandong Agricultural University, Taian, Shandong, 271018, China
- College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Deng-Ji Jiang
- College of Plant Protection, South China Agricultural University, Guangzhou, 510000, China
| | - Heng Tang
- National Key Laboratory of Wheat Breeding, Shandong Agricultural University, Taian, Shandong, 271018, China.
- College of Agriculture, Shandong Agricultural University, Taian, Shandong, 271018, China.
| | - Fang Wang
- National Key Laboratory of Wheat Breeding, Shandong Agricultural University, Taian, Shandong, 271018, China.
- College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China.
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Liu N, Shang W, Guan M, Xiao J, Tian G, Ma B, Shang W, Li X, Zhao S, Li C, Cheng K, Zheng W. Phosphate deficiency responsive TaSPX3 is involved in the regulation of shoot phosphorus in Arabidopsis plants. Plant Physiol Biochem 2024; 206:108215. [PMID: 38029619 DOI: 10.1016/j.plaphy.2023.108215] [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: 10/16/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023]
Abstract
SPX (SYG/PHO81/XPR1) domain genes have been reported to play vital roles in the Phosphorus (Pi) signaling network in Arabidopsis thaliana and rice. However, the functions of SPX proteins in wheat remain largely unknown. In this study, the full-length cDNA sequence of the TaSPX3 gene was cloned from the common wheat variety Zhengmai9023. The expression of TaSPX3 was up-regulated in eight different genotypes of wheat under low phosphorus (LP) stress, indicating that TaSPX3 responds to Pi limitation in multiple wheat genotypes. The transcription level of TaSPX3 was also detected in the absence of seven different elements, showing certain specificity for Pi deficiency in wheat. Over expressing TaSPX3 in Arabidopsis can alleviate Pi deficiency symptoms at the seedling stage and promote the growth of plant, and advance the flowering period at the adult stage. The expression of 7 genes associated with the Pi starvation signal pathways was analyzed using qRT-PCR. The results showed that TaSPX3, along with AtSPX1, AtRNS1, AtIPS1, AtPAP2, AtPAP17 and AtAT4, were all induced by Pi deficiency. This study reveals that the TaSPX3 gene in wheat is involved in the response to phosphorus stress and may affect shoot phosphorus levels through AT4 or PAPs-related pathways. Overall, our study provides new insights into the regulation of plant response under LP conditions and the molecular mechanism underlying the role of the wheat SPX gene in coping with LP stress.
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Affiliation(s)
- Na Liu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, 450002, Zhengzhou, China
| | - Wenyan Shang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, 450002, Zhengzhou, China
| | - Mengxin Guan
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, 450002, Zhengzhou, China
| | - Jibin Xiao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, 450002, Zhengzhou, China
| | - Guangxiang Tian
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, 450002, Zhengzhou, China
| | - Baozhan Ma
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, 450002, Zhengzhou, China
| | - Wenjing Shang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, 450002, Zhengzhou, China
| | - Xu Li
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, 450002, Zhengzhou, China
| | - Shijia Zhao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, 450002, Zhengzhou, China
| | - Chuang Li
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, 450002, Zhengzhou, China
| | - Kun Cheng
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, 450002, Zhengzhou, China.
| | - Wenming Zheng
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, 450002, Zhengzhou, China.
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Ma J, Nie Y, Zhang L, Xu Y. The evolutionary mechanism and function analysis of two subgroups of histamine-producing and non-histamine-producing Tetragenococcus halophilus. Food Res Int 2024; 176:113744. [PMID: 38163696 DOI: 10.1016/j.foodres.2023.113744] [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: 08/22/2023] [Revised: 11/07/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024]
Abstract
Tetragenococcus halophilus is a halophilic bacterium that existed in the fermentation of soy sauce and miso for flavor production and probiotic benefits. However, it is composed of two subgroups, histamine-producing and non-histamine-producing, with the former causing histamine accumulation and offering risks to food safety. Exploring the evolutionary mechanisms and physiological function of histamine-biosynthesis is of significance for understanding the formative mechanism of T. halophilus's strain-specificity and is helpful for microbial control. Using systematic genomic analysis, we found that plasmid acquisition and loss is the evolutionary form resulting in the two subgroups of T. halophilus. Two plasmids, plasmid α with 30 kb and plasmid β with 4 kb existed in histamine-producing T. halophilus. We investigated the whole genetic information and proposed their genetic function in both two plasmids. The acquisition of histamine-producing plasmid enhanced the acid tolerance of histamine-producing T. halophilus but did not affect salt tolerance. More interestingly, we found that the existence of plasmid will promote the co-culture growth of T. halophilus. This study deepens our understanding of the formative mechanism of microbial species diversity, and provides our knowledge of the physiological function of histamine-producing plasmids.
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Affiliation(s)
- Jinjin Ma
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Yao Nie
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Lijie Zhang
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China.
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
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Li L, Zhang X, Ding F, Hou J, Wang J, Luo R, Mao W, Li X, Zhu H, Yang L, Li Y, Hu J. Genome-wide identification of the melon (Cucumis melo L.) response regulator gene family and functional analysis of CmRR6 and CmPRR3 in response to cold stress. J Plant Physiol 2024; 292:154160. [PMID: 38147808 DOI: 10.1016/j.jplph.2023.154160] [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: 03/10/2023] [Revised: 12/03/2023] [Accepted: 12/07/2023] [Indexed: 12/28/2023]
Abstract
The response regulator (RR) gene family play crucial roles in cytokinin signal transduction, plant development, and resistance to abiotic stress. However, there are no reports on the identification and functional characterization of RR genes in melon. In this study, a total of 18 CmRRs were identified and classified into type A, type B, and clock PRRs, based on phylogenetic analysis. Most of the CmRRs displayed tissue-specific expression patterns, and some were induced by cold stress according to two RNA-seq datasets. The expression patterns of CmRR2/6/11/15 and CmPRR2/3 under cold treatment were confirmed by qRT-PCR. Subcellular localization assays indicated that CmRR6 and CmPRR3 were primarily localized in the nucleus and chloroplast. Furthermore, when either CmRR6 or CmPRR3 were silenced using tobacco ringspot virus (TRSV), the cold tolerance of the virus-induced gene silencing (VIGS) melon plants were significantly enhanced, as evidenced by measurements of chlorophyll fluorescence, ion leakage, reactive oxygen, proline, and malondialdehyde levels. Additionally, the expression levels of CmCBF1, CmCBF2, and CmCBF3 were significantly increased in CmRR6-silenced and CmPRR3-silenced plants under cold treatment. Our findings suggest that CmRRs contribute to cold stress responses and provide new insights for further pursuing the molecular mechanisms underlying CmRRs-mediated cold tolerance in melon.
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Affiliation(s)
- Lili Li
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiuyue Zhang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China
| | - Fei Ding
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China
| | - Juan Hou
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China; Research Center of Cucurbit Germplasm Enhancement and Utilization of Henan Province, Zhengzhou, 450046, China
| | - Jiyu Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China
| | - Renren Luo
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China
| | - Wenwen Mao
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China; Research Center of Cucurbit Germplasm Enhancement and Utilization of Henan Province, Zhengzhou, 450046, China
| | - Xiang Li
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China; International Joint Laboratory of Henan Horticultural Crop Biology, Pingan Avenue 218, Zhengdong New District, Zhengzhou, 450046, China
| | - Huayu Zhu
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China; International Joint Laboratory of Henan Horticultural Crop Biology, Pingan Avenue 218, Zhengdong New District, Zhengzhou, 450046, China
| | - Luming Yang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China; International Joint Laboratory of Henan Horticultural Crop Biology, Pingan Avenue 218, Zhengdong New District, Zhengzhou, 450046, China
| | - Ying Li
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Jianbin Hu
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, China; Research Center of Cucurbit Germplasm Enhancement and Utilization of Henan Province, Zhengzhou, 450046, China.
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Wu Q, Huang C, Chen R, Li D, Zhang G, Yu H, Li Y, Song B, Zhang N, Li B, Chu X. Transcriptional and functional analysis of plasma exosomal microRNAs in acute viral myocarditis. Genomics 2024; 116:110775. [PMID: 38163573 DOI: 10.1016/j.ygeno.2023.110775] [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: 07/25/2023] [Revised: 11/25/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
AIM To assess the differential expression profiles of exosome-derived microRNA (miRNA) and reveal their potential functions in patients with acute viral myocarditis (AVMC). MATERIALS & METHODS Peripheral blood samples were collected from 9 patients diagnosed with AVMC and 9 healthy controls (HC) in the Affiliated Hospital of Qingdao University from July 2021 to September 2022. The exosomal miRNA expression were tested using RNA high-throughput sequencing. We conducted the GO and KEGG functional analysis to predict the potential molecular, biological functions and related signaling pathways of miRNAs in exosomes. Target genes of exosomal miRNAs were predicted and miRNA-target gene network was mapped using gene databases. Differentially expressed exosomal miRNAs were selected and their expression levels were detected by quantitative real-time polymerase chain reaction (qRT-PCR) to verify the sequencing results. RESULTS P < 0.05 and Fold Change>2 were considered as cut-off value to screen miRNAs that were differently expressed. This study identified 14 upregulated and 14 downregulated exosome-derived miRNAs. GO and KEGG analysis showed that differentially expressed miRNAs may be related to β-catenin binding, DNA transcription activities, ubiquitin ligase, PI3K-Akt, FoxO, P53, MAPK, and etc.. The target genes of differentially expressed miRNAs were predicted using gene databases. Real-time PCR confirmed the upregulation of hsa-miR-548a-3p and downregulation of hsa-miR-500b-5p in AVMC. CONCLUSIONS Hsa-miR-548a-3p and hsa-miR-500b-5p could serve as a promising biomarker of AVMC. Exosomal miRNAs may have substantial roles in the mechanisms of AVMC.
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Affiliation(s)
- Qinchao Wu
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao 266100, China
| | - Chao Huang
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao 266100, China
| | - Ruolan Chen
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao 266100, China
| | - Daisong Li
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao 266100, China
| | - Guoliang Zhang
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao 266100, China
| | - Haichu Yu
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao 266100, China
| | - Yonghong Li
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao 266100, China
| | - Bingxue Song
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao 266100, China
| | - Ning Zhang
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao 266100, China
| | - Bing Li
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, 266071 Qingdao, China; Department of Dermatology, The Affiliated Haici Hospital of Qingdao University, Qingdao 266000, China.
| | - Xianming Chu
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao 266100, China; The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao 266000, China.
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Lu Y, Li T, Zhao X, Wang M, Huang J, Huang Z, Teixeira da Silva JA, Duan J, Si C, Zhang J. Identification of the CONSTANS-like family in Cymbidium sinense, and their functional characterization. BMC Genomics 2023; 24:786. [PMID: 38110864 PMCID: PMC10729429 DOI: 10.1186/s12864-023-09884-3] [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: 08/03/2023] [Accepted: 12/08/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Cymbidium sinense is an orchid that is typically used as a potted plant, given its high-grade ornamental characteristics, and is most frequently distributed in China and SE Asia. The inability to strictly regulate flowering in this economically important potted and cut-flower orchid is a bottleneck that limits its industrial development. Studies on C. sinense flowering time genes would help to elucidate the mechanism regulating flowering. There are very few studies on the genetic regulation of flowering pathways in C. sinense. Photoperiod significantly affects the flowering of C. sinense, but it was unknown how the CONSTANS gene family is involved in regulating flowering. RESULTS In this study, eight CONSTANS-like genes were identified and cloned. They were divided into three groups based on a phylogenetic analysis. Five representative CsCOL genes (CsCOL3/4/6/8/9) were selected from the three groups to perform expression characterization and functional study. CsCOL3/4/6/8/9 are nucleus-localized proteins, and all five CsCOL genes were expressed in all organs, mainly in leaves followed by sepals. The expression levels of CsCOL3/4 (group I) were higher in all organs than other CsCOL genes. Developmental stage specific expression revealed that the expression of CsCOL3/4/9 peaked at the initial flowering stage. In contrast, the transcript level of CsCOL6/8 was highest at the pedicel development stage. Photoperiodic experiments demonstrated that the transcripts of the five CsCOL genes exhibited distinct diurnal rhythms. Under LD conditions, the overexpression of CsCOL3/4 promoted early flowering, and CsCOL6 had little effect on flowering time, whereas CsCOL8 delayed flowering of Arabidopsis thaliana. However, under SD conditions, overexpression of CsCOL4/6/8 promoted early flowering and the rosette leaves growth, and CsCOL3 induced flower bud formation in transgenic Arabidopsis. CONCLUSION The phylogenetic analysis, temporal and spatial expression patterns, photoperiodic rhythms and functional study indicate that CsCOL family members in C. sinense were involved in growth, development and flowering regulation through different photoperiodic pathway. The results will be useful for future research on mechanisms pertaining to photoperiod-dependent flowering, and will also facilitate genetic engineering-based research that uses Cymbidium flowering time genes.
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Affiliation(s)
- Youfa Lu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Tengji Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaolan Zhao
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Mingjun Wang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Jiexian Huang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Ziqin Huang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | | | - Jun Duan
- Key laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Can Si
- Key laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Jianxia Zhang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
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Liu P, Li W, Peng Y, Han S, Liang Z, Cen Y, Li X, Wang P, Lv H, Zhang Q, Chen H, Lin J. Molecular cloning, expression, and functional analysis of a putative lectin from the pearl oyster (Pinctada fucata, Gould 1850). Fish Shellfish Immunol 2023; 143:109215. [PMID: 37951320 DOI: 10.1016/j.fsi.2023.109215] [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: 06/16/2023] [Revised: 11/03/2023] [Accepted: 11/05/2023] [Indexed: 11/13/2023]
Abstract
Marine lectins are a group of proteins that possess specific carbohydrate recognition and binding domains. They exhibit various activities, including antimicrobial, antitumor, antiviral, and immunomodulatory effects. In this study, a novel galectin-binding lectin gene named PFL-96 (GenBank: OQ561753.1) was cloned from Pinctada fucata. The PFL-96 gene has an open reading frame of 324 base pairs (bp) and encodes a protein comprising 107 amino acids. The protein has a molecular weight of 11.95 kDa and an isoelectric point of 9.27. It contains an N-terminal signal peptide and a galactose-binding lectin domain. The sequence identity to lectin proteins from fish, echinoderms, coelenterates, and shellfish ranges from 31.90 to 40.00 %. In the phylogenetic analysis, it was found that the PFL-96 protein is closely related to the lectin from Pteria penguin. The PFL-96 recombinant protein exhibited coagulation activity on 2 % rabbit red blood cells at a concentration of ≥8 μg/mL. Additionally, it showed significant hemolytic activity at a concentration of ≥32 μg/mL. The PFL-96 recombinant protein exhibited significant antibacterial activity against Bacillus subtilis, Staphylococcus aureus, Candida albicans, and Vibrio alginolyticus, with minimum inhibitory concentrations (MIC) of 4, 8, 16, and 16 μg/mL, respectively. The minimum bactericidal concentrations (MBC) were determined to be 8, 16, 32, and 32 μg/mL, respectively. Furthermore, the PFL-96 recombinant protein exhibited inhibitory effects on the proliferation of Hela tumor cells, HepG2 tumor cells, and C666-1 tumor cells, with IC50 values of 7.962, 8.007, and 9.502 μg/mL, respectively. These findings suggest that the recombinant protein PFL-96 exhibits significant bioactivity in vitro, contributing to a better understanding of the active compounds found in P. fucata. The present study establishes a fundamental basis for further investigation into the mechanism of action and structural optimization of the recombinant protein PFL-96. The aim is to develop potential candidates for antibacterial and anti-tumor agents.
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Affiliation(s)
- Peng Liu
- Comprehensive Laboratory of Medical Innovation, School of Basic Medical Science, Guangxi University of Chinese Medicine, Nanning, China.
| | - Wenyue Li
- Comprehensive Laboratory of Medical Innovation, School of Basic Medical Science, Guangxi University of Chinese Medicine, Nanning, China
| | - Yue Peng
- Comprehensive Laboratory of Medical Innovation, School of Basic Medical Science, Guangxi University of Chinese Medicine, Nanning, China
| | - Siyin Han
- Comprehensive Laboratory of Medical Innovation, School of Basic Medical Science, Guangxi University of Chinese Medicine, Nanning, China
| | - Zhongxiu Liang
- Comprehensive Laboratory of Medical Innovation, School of Basic Medical Science, Guangxi University of Chinese Medicine, Nanning, China
| | - Yanhui Cen
- Comprehensive Laboratory of Medical Innovation, School of Basic Medical Science, Guangxi University of Chinese Medicine, Nanning, China
| | - Xinrong Li
- Comprehensive Laboratory of Medical Innovation, School of Basic Medical Science, Guangxi University of Chinese Medicine, Nanning, China
| | - Peiyan Wang
- Comprehensive Laboratory of Medical Innovation, School of Basic Medical Science, Guangxi University of Chinese Medicine, Nanning, China
| | - Huiying Lv
- Comprehensive Laboratory of Medical Innovation, School of Basic Medical Science, Guangxi University of Chinese Medicine, Nanning, China
| | - Qingying Zhang
- Comprehensive Laboratory of Medical Innovation, School of Basic Medical Science, Guangxi University of Chinese Medicine, Nanning, China
| | - Honglin Chen
- Comprehensive Laboratory of Medical Innovation, School of Basic Medical Science, Guangxi University of Chinese Medicine, Nanning, China
| | - Jiang Lin
- Comprehensive Laboratory of Medical Innovation, School of Basic Medical Science, Guangxi University of Chinese Medicine, Nanning, China.
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Tan K, Dong Y, Tan K, Lim LS, Waiho K, Chen J, Xu P, Kwan KY. siRNA Silencing of FpVtg Induces Ovarian Cell Apoptosis in Redtail Prawn, Fenneropenaeus penicillatus. Mar Biotechnol (NY) 2023; 25:1176-1190. [PMID: 38010485 DOI: 10.1007/s10126-023-10269-6] [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] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023]
Abstract
Inadequate gonadal maturation and poor spawning performance increasingly threaten the sustainability of shrimp aquaculture. Unraveling the mechanisms regulating ovarian development and maturation hence is critical to address industry challenges. Vitellogenin (Vtg), a precursor of yolk protein found in the hepatopancreas and ovary of shrimp, plays a key role in facilitating shrimp's oocyte maturation and embryonic development after oviposition. This study found that FpVtg was specifically expressed in F. penicillatus hepatopancreas and ovary. FpVtg was localized predominantly in the oocyte cytoplasm and distributed uniformly in the hepatopancreas tissue. Silencing FpVtg led to apoptosis in both hepatopancreas and ovary tissues. Furthermore, FpVtg depletion upregulated the expression of ovarian peritrophin 1, ovarian peritrophin 2, serine proteinase inhibitor 6, and juvenile hormone esterase-like carboxylesterase 1, while downregulated that of vitellogenin, delta-9 desaturase, and insulin-like receptor. KEGG pathway analysis implicated such as PI3K-AKT signaling, RNA transport, ECM-receptor interaction, hippo signaling, oocyte meiosis, and apoptosis were enriched and involved in ovarian development. These findings have provided insights into the FpVtg's reproductive role and the associated regulatory genes and pathways in F. penicillatus. This knowledge can contribute to establishing strategies to improve the breeding and aquaculture production of F. penicillatus by elucidating its vitellogenesis regulation in redtail prawn and other penaeid species. Further characterization of the implicated pathways and genes will clarify the intricacies underlying ovarian maturation.
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Affiliation(s)
- Kianann Tan
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou City, 535011, Guangxi, China
| | - Yaxin Dong
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou City, 535011, Guangxi, China
| | - Karsoon Tan
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou City, 535011, Guangxi, China
| | - Leong-Seng Lim
- Borneo Marine Research Institute, Universiti Malaysia Sabah, Kota Kinabalu City, Sabah, Malaysia
| | - Khor Waiho
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus City, 21030, Terengganu, Malaysia
| | - Jing Chen
- Zhejiang Institute of Freshwater Fisheries, Huzhou City, 313001, China
| | - Peng Xu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou City, 535011, Guangxi, China.
| | - Kit Yue Kwan
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou City, 535011, Guangxi, China.
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Qi B, Wang HY, Ma X, Chi YF, Gui C. Identification of the Key Genes of Immune Infiltration in Dilated Cardiomyopathy. Int Heart J 2023; 64:1054-1064. [PMID: 37967988 DOI: 10.1536/ihj.23-182] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
Dilated cardiomyopathy (DCM) is a common cause of heart failure. In this study, we screened the immune infiltration-related genes associated with DCM to explore the potential molecular mechanisms and provide a basis for the early diagnosis and development of new immunotherapeutic targets. A dataset related to DCM was downloaded from the Gene Expression Omnibus (GEO) database. R software was applied to the genetic differential analysis of patients with DCM and healthy individuals, and the obtained differential expressed genes (DEGs) were screened for differentially expressed immune-related genes (DEIRGs) after comparison with the immune microsatellite database. Gene functional analysis established a protein interaction network (PPI). The immune infiltration in patients with DCM versus normal controls was assessed using the CIBERSORT algorithm, the hub genes were screened using the MOCDE app, and the hubs were validated in multiple datasets. A total of 246 DEGs were screened (adj. P < 0.05 and |logFC| > 0.3), and a total of 170 DEIRGs were compared. Gene Ontology analysis showed significant (adj. P < 0.05) Biological Process entries of 591, Cellular Component of 10, and Molecular Function of 39; Kyoto Encyclopedia of Genes and Genomes showed 20 significant entries, mainly focused on cytokines involved in immune-related response, etc. A protein interaction network comprising 28 hub DEGs was constructed in combination with the PPI network interactions. DEIRG was mainly distributed in the T-cell receptor pathway by immune infiltration detection analysis, and significant changes in central memory T-cells were found by analyzing T-cell-related subpathways, where INSR, HLA-B, IFITM1, and HBEGF were significantly differentially expressed. We selected 632 hospitalized patients for validation and found that INSR and HLA-B expression were associated with DCM development by Nomogram. The expression of HLA-B in peripheral blood T-cells was higher in DCM patients than in the normal group, as verified by qRT-PCR. However, the detailed mechanism needs to be further explored.
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Affiliation(s)
- Bin Qi
- Department of Cardiology, First Affiliated Hospital, Guangxi Medical University
| | - Hai-Yan Wang
- Department of Cardiology, First Affiliated Hospital, Guangxi Medical University
| | - Xiao Ma
- Department of Cardiology, First Affiliated Hospital, Guangxi Medical University
| | - Yu-Feng Chi
- Department of Cardiology, First Affiliated Hospital, Guangxi Medical University
| | - Chun Gui
- Department of Cardiology, First Affiliated Hospital, Guangxi Medical University
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Gao B, Liu X, Feng Z, Wu J, Wang J. Potentilla sericea stress-responsive spermine synthase PsSPMS enhances cadmium tolerance in Arabidopsis thaliana. Chemosphere 2023; 342:140194. [PMID: 37717914 DOI: 10.1016/j.chemosphere.2023.140194] [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: 05/18/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/19/2023]
Abstract
Potentilla sericea is resistant and tolerates rough management. It is an excellent garden groundcover for ecological restoration and soil consolidation for slope protection. Polyamines have functions such as promoting tissue growth and physiological resistance, while spermine synthase catalyzes the production of spermine. The PsSPMS gene from Potentilla sericea was cloned and transformed into Arabidopsis thaliana to study the response of transgenic Arabidopsis thaliana to cadmium stress. The results showed that the contents of spermidine, spermine as well as glutathione were higher in PsSPMS overexpressing Arabidopsis thaliana than the control, while the contents of putrescine were less than the control. Net photosynthetic rate, stomatal conductance, chlorophyll content, water use efficiency, electron transfer rate, PSII-related parameters, proline content, superoxide dismutase, and glutathione reductase activities were higher in PsSPMS overexpressing Arabidopsis thaliana than the control, while malondialdehyde, superoxide anion, and hydrogen peroxide contents were lower than the control. Correlation analysis showed significant differences between the indicators (P < 0.05 and P < 0.01). Expression of AtSPMS, AtSPD3, AtGSH2 and AtGR in transgenic Arabidopsis thaliana was higher than that of the control. Therefore, this study provides a genetic reference for the cultivation of cadmium-tolerant plants through genetic engineering and lays the foundation for further research on cadmium-tolerant Potentilla sericea.
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Affiliation(s)
- Bing Gao
- Northeast Forestry University, Hexing Road, Harbin, Heilongjiang Province, 150040, PR China
| | - Xiangyue Liu
- Northeast Forestry University, Hexing Road, Harbin, Heilongjiang Province, 150040, PR China
| | - Zhenghong Feng
- Northeast Forestry University, Hexing Road, Harbin, Heilongjiang Province, 150040, PR China
| | - Jianhui Wu
- Northeast Forestry University, Hexing Road, Harbin, Heilongjiang Province, 150040, PR China.
| | - Jinghong Wang
- Northeast Forestry University, Hexing Road, Harbin, Heilongjiang Province, 150040, PR China.
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Tan K, Waiho K, Tan K, Qiao Y, Lim LS, Yang X, Wen Y, Xu P, Peng Y, Ma X, Kwan KY. Silencing of novel TtVtg6-like induced ovarian cell apoptosis in ancient chelicerate Tachypleus tridentatus. Biochem Biophys Res Commun 2023; 679:66-74. [PMID: 37673004 DOI: 10.1016/j.bbrc.2023.08.066] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/19/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
Vitellogenin (Vtg) serves as the precursor of yolk protein and exhibits widespread distribution in tissues, including in the ovary of both vertebrates and invertebrates. Vtg plays a critical role in facilitating oocyte maturation and embryonic development following oviposition. In this study, we have successfully elucidated the complete transcript sequence of TtVtg6-like from an ancient chelicerate Tachypleus tridentatus. The TtVtg6-like transcript encompassed a length of 4887 bp and encoded 1629 amino acids residues. Notably, TtVtg6-like was found to contain 25 exons. Furthermore, the molecular weight and isoelectric point of TtVtg6-like were determined to be 191.6 KDa and 6.73, respectively. Subsequent mRNA expression analysis demonstrated the specific expression of TtVtg6-like in ovary and yellow connective tissue. In addition, TtVtg6-like was located and distributed in both ovary and yellow connective tissue. Intriguingly, employing an siRNA approach to silence TtVtg6-like resulted in a decrease in TtVtg6-like transcription levels. Concomitantly, TtVtg6-like silencing led to increase production of ROS, ultimately resulting in DNA damage and cell apoptosis within the ovarian primary cell. The induction of apoptosis ovarian primary cells due to TtVtg6-like silencing was further corroborated through TUNEL assay and flow cytometry analysis. Overall, our findings underscore the significance of TtVtg6-like in ovarian cell development, revealing its potential association with ovarian cell apoptosis. Consequently, the insights gained from this study contribute to the future exploration of vitellogenesis and ovarian development in T. tridentatus.
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Affiliation(s)
- Kianann Tan
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, Guangxi, China
| | - Khor Waiho
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, 21030, Terengganu, Malaysia
| | - Karsoon Tan
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, Guangxi, China
| | - Ying Qiao
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, 536000, Guangxi, China
| | - Leong-Seng Lim
- Borneo Marine Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Xin Yang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, Guangxi, China
| | - Yulong Wen
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, Guangxi, China
| | - Peng Xu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, Guangxi, China
| | - Ya Peng
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, Guangxi, China
| | - Xiaowan Ma
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, 536000, Guangxi, China.
| | - Kit Yue Kwan
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, Guangxi, China.
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Bekele-Alemu A, Ligaba-Osena A. Comprehensive in silico analysis of the underutilized crop tef (Eragrostis tef (Zucc.) Trotter) genome reveals drought tolerance signatures. BMC Plant Biol 2023; 23:506. [PMID: 37865758 PMCID: PMC10589971 DOI: 10.1186/s12870-023-04515-1] [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] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/05/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Tef (Eragrostis tef) is a C4 plant known for its tiny, nutritious, and gluten-free grains. It contains higher levels of protein, vitamins, and essential minerals like calcium (Ca), iron (Fe), copper (Cu), and zinc (Zn) than common cereals. Tef is cultivated in diverse ecological zones under diverse climatic conditions. Studies have shown that tef has great diversity in withstanding environmental challenges such as drought. Drought is a major abiotic stress severely affecting crop productivity and becoming a bottleneck to global food security. Here, we used in silico-based functional genomic analysis to identify drought-responsive genes in tef and validated their expression using quantitative RT-PCR. RESULTS We identified about 729 drought-responsive genes so far reported in six crop plants, including rice, wheat, maize, barley, sorghum, pearl millet, and the model plant Arabidopsis, and reported 20 genes having high-level of GO terms related to drought, and significantly enriched in several biological and molecular function categories. These genes were found to play diverse roles, including water and fluid transport, resistance to high salt, cold, and drought stress, abscisic acid (ABA) signaling, de novo DNA methylation, and transcriptional regulation in tef and other crops. Our analysis revealed substantial differences in the conserved domains of some tef genes from well-studied rice orthologs. We further analyzed the expression of sixteen tef orthologs using quantitative RT-PCR in response to PEG-induced osmotic stress. CONCLUSIONS The findings showed differential regulation of some drought-responsive genes in shoots, roots, or both tissues. Hence, the genes identified in this study may be promising candidates for trait improvement in crops via transgenic or gene-editing technologies.
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Affiliation(s)
- Abreham Bekele-Alemu
- Laboratory of Plant Molecular Biology and Biotechnology, Department of Biology, University of North Carolina Greensboro, Greensboro, NC, USA
| | - Ayalew Ligaba-Osena
- Laboratory of Plant Molecular Biology and Biotechnology, Department of Biology, University of North Carolina Greensboro, Greensboro, NC, USA.
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Liu E, Zhu S, Du M, Lyu H, Zeng S, Liu Q, Wu G, Jiang J, Dang X, Dong Z, Hong D. LAX1, functioning with MADS-box genes, determines normal palea development in rice. Gene 2023; 883:147635. [PMID: 37442304 DOI: 10.1016/j.gene.2023.147635] [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: 03/08/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
Abstract
Normal floral organ development in rice is necessary for grain formation. Many MADS-box family genes that belong to ABCDE model have been widely implicated in rice flower development. The LAX1 allele encodes a plant-specific basic helix-loop-helix (bHLH) transcription factor, which is the main regulator of axillary meristem formation in rice. However, the molecular mechanisms of LAX1 allele together with MADS-box family genes underlying palea development have not been reported. We found a short palea mutant plant in a population of indica rice variety 9311 treated with cobalt 60. We report the map-based cloning and characterization of lax1-7, identified as a new mutant allele of the LAX1 locus, and the role of its wild-type allele LAX1 in rice palea development. Through complementary experiments, combined with genetic and molecular biological analyses, the function of the LAX1 allele was determined. We showed that LAX1 allele is expressed specifically in young spikelets and encodes a nucleus-localized protein. In vitro and in vivo experiments revealed that the LAX1 protein physically interacts with OsMADS1, OsMADS6 and OsMADS7. The LAX1 allele is pleiotropic for the maintenance of rice palea identity via cooperation with MADS-box genes and other traits, including axillary meristem initiation, days to heading, plant height, panicle length and spikelet fertility.
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Affiliation(s)
- Erbao Liu
- College of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Shangshang Zhu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingyu Du
- College of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Huineng Lyu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Siyuan Zeng
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiangming Liu
- Chongqing Academy of Agricultural Sciences, Chongqing 401329, China
| | - Guocan Wu
- Ningde Institute of Agricultural Sciences, Ningde 355017, China
| | - Jianhua Jiang
- Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Xiaojing Dang
- Anhui Academy of Agricultural Sciences, Hefei 230001, China
| | - Zhiyao Dong
- College of Life Sciences, Jilin Normal University, Jilin 136000, China
| | - Delin Hong
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China.
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Opoku – Mensah S. An assessment of the structure of shea global value chain in Ghana and implication for policy development. Heliyon 2023; 9:e20219. [PMID: 37810873 PMCID: PMC10550592 DOI: 10.1016/j.heliyon.2023.e20219] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
The global value chain for shea has witnessed major transformations in the last two decades. This study was aimed at providing a detailed understanding of the structure of the shea value chain in Ghana. Data were collected primarily from primary source and secondary sources. A total of 820 upstream actors, 20 aggregators, 2 processing companies and other experts were interviewed using both closed-ended and open-ended questionnaires to gather qualitative and quantitative data. The study employed the value chain framework to analyse the structure of the shea value chain in Ghana. Data analysis was primarily descriptive in nature. A value chain map, schematic diagram, and flow charts were generated to show the linkages between actors and the flow of resources, materials, products, information, and funds. The results show that the shea value chain is highly gendered, with women at the base of the chain, working as shea kernel producers and processors of crude shea butter, using mainly traditional methods, hence output is sub-optimal. The mid-stream actors were all males, whose main function involves aggregating shea kernels across several communities for industrial processors and export companies. Processing companies, using mechanised methods, process and export several derivatives of shea (shea grits, shea butter, stearin, and olein) to mainly to high-end markets in the E.U and Asia. Though female participation in the shea global value chain is prominent, their output is way too low at the current level to make significant impact. Policy focus must be on supporting upstream actors through the provision of improved processing facilities, community infrastructure, and skills training to enhance the capacity of upstream actors to improve their performance.
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Affiliation(s)
- Stephen Opoku – Mensah
- Department of Agropreneurship, Kumasi Technical University, P. O. Box 854, Kumasi, Ghana
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Morris C, McCormack JV, Perrin J. Multiple Isolated Functions of Problematic Behavior: A Case Study. Behav Anal Pract 2023; 16:873-878. [PMID: 37680337 PMCID: PMC10480105 DOI: 10.1007/s40617-023-00777-1] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2023] [Indexed: 01/21/2023] Open
Abstract
Multiple isolated functions of problematic behavior are distinct from synthesized functions. Limited research has focused on the considerations of assessing and treating multiple isolated functions of problematic behavior. This case study utilized traditional functional analysis procedures to identify the functions of the targeted problematic behavior and a multiple baseline across functional contexts design to evaluate a function-based treatment. The nuances of assessing and treating multiple isolated functions are discussed.
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Affiliation(s)
- Cody Morris
- Department of Psychology, Salve Regina University, 100 Ochre Point Avenue, Newport, RI 02840 USA
| | - Jocelyn V. McCormack
- Department of Psychology, Salve Regina University, 100 Ochre Point Avenue, Newport, RI 02840 USA
- Pathways Strategic Teaching Center, Coventry, RI USA
| | - Jesse Perrin
- Pathways Strategic Teaching Center, Coventry, RI USA
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38
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Strohmeier CW, Goetzel A, Deinlein S, Schmidt JD. Repetitive Speech and Problem Behavior: Functional Analysis of Precurrent Contingencies. Behav Anal Pract 2023; 16:745-754. [PMID: 37680334 PMCID: PMC10480119 DOI: 10.1007/s40617-022-00743-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2022] [Indexed: 10/14/2022] Open
Abstract
When mands and problem behavior co-occur within an individual's repertoire, a functional analysis of precurrent contingencies helps to identify any relation between the two responses, as well as the function of problem behavior. Repetitive behaviors may function similarly to mands and also co-occur with problem behavior; particularly when repetitive behavior is blocked, or when caregivers refrain from participating in repetitive behavior episodes (e.g., the repetitive behavior involves a verbal or physical interaction with a caregiver). The current study presents assessment and treatment results for two participants diagnosed with autism, who demonstrated repetitive speech and problem behavior. Informal observations suggested that problem behavior occurred when an adult failed to emit a specific response to the participant's repetitive speech. Functional analysis results confirmed the informal observations and suggested that problem behavior functioned as a precurrent response to increase the probability of reinforcement for repetitive speech. We report treatment results and discuss the application of precurrent contingency analyses for problem behavior and repetitive behavior.
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Affiliation(s)
- Craig W. Strohmeier
- Neurobehavioral Unit Programs, Department of Behavioral Psychology, Kennedy Krieger Institute, 707 North Broadway, Baltimore, MD 21205 USA
- Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Amanda Goetzel
- Neurobehavioral Unit Programs, Department of Behavioral Psychology, Kennedy Krieger Institute, 707 North Broadway, Baltimore, MD 21205 USA
| | - Sara Deinlein
- Neurobehavioral Unit Programs, Department of Behavioral Psychology, Kennedy Krieger Institute, 707 North Broadway, Baltimore, MD 21205 USA
| | - Jonathan D. Schmidt
- Neurobehavioral Unit Programs, Department of Behavioral Psychology, Kennedy Krieger Institute, 707 North Broadway, Baltimore, MD 21205 USA
- Johns Hopkins University School of Medicine, Baltimore, MD USA
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Duan X, Wen Y, Wu P, Peng J, Zhou Y, Zhu G, Li D, Ru Y, Yang W, Zheng H. Functional characterization of African swine fever virus I329L gene by transcriptome analysis. Vet Microbiol 2023; 284:109836. [PMID: 37574636 DOI: 10.1016/j.vetmic.2023.109836] [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: 04/14/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/15/2023]
Abstract
African swine fever (ASF) is an acute, severe, and highly contagious disease caused by the African swine fever virus (ASFV), which infects domestic pigs and wild boars. The incidence and mortality rates of swine infected with virulent strains of ASFV can reach up to 100%. The large genome, its complex structure, multiple genotypes, and a lack of understanding regarding ASFV gene function are serious obstacles to the development of safe and effective vaccines. Here, ASFV I329L was identified as a relatively conserved gene that is expressed during the late stage of infection. A recombinant virus with I329L gene deletion (ASFV CN/GS/2018-ΔI329L) was produced by replacing I329L with an enhanced green fluorescent protein (EGFP) cassette. In order to explore the function of the ASFV I329L gene, transcriptome sequencing (RNA-seq) was performed on porcine alveolar macrophages (PAMs) infected with ASFV CN/GS/2018 and ASFV CN/GS/2018-ΔI329L. GO functional and KEGG pathway analyses were performed to analyze differentially expressed genes, and different alternative splicing (AS) events were also analyzed. We compared the sequencing data for each sample with the ASFV CN/GS/2018 reference sequence. Interestingly, we found 3 and 1 up-regulated genes and 12 and 19 down-regulated genes at 12 and 24 h post-infection, respectively. In addition, we verified the expression of 5 up-regulated and 5 down-regulated genes by RT-qPCR, and the results were consistent with those obtained based on RNA-seq. In summary, the results obtained in this study provide new insights for further elucidation of ASFV proteins and ASFV-host interactions. These findings will contribute to implementing a comprehensive strategy for controlling the spread of ASF.
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Affiliation(s)
- Xianghan Duan
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yuan Wen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Panxue Wu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jiangling Peng
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yanlong Zhou
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Guoqiang Zhu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Dan Li
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yi Ru
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Wenping Yang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.
| | - Haixue Zheng
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.
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40
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Metras RL, Hanley GP, Carbone MJ. Distance-Based Collaborations for Assessing and Treating Challenging Behavior. J Autism Dev Disord 2023:10.1007/s10803-023-06085-5. [PMID: 37620690 DOI: 10.1007/s10803-023-06085-5] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2023] [Indexed: 08/26/2023]
Abstract
An interview-informed synthesized contingency analysis (IISCA; Hanley et al. in J Appl Behav Anal 47:16-36, 2014) and related skill-based treatment process can result in socially valid outcomes for clients exhibiting severe challenging behavior when implemented by professionals and then transferred to parents (e.g., Santiago et al. in J Autism Dev Disord 46:797-811, 2016). However, many families do not have access to professionals trained to implement functional analyses or function-based treatments (Deochand & Fuqua Behav Anal Pract 9:243-252, 2016). Experimenters in the present study coached three parents of children with autism exhibiting severe challenging behavior through implementing an IISCA and resulting skill-based treatment process through distance-based collaborative consulting. All parents achieved differentiated functional analyses, taught their children to emit functional replacement skills, and reduced challenging behavior relative to baseline.
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Affiliation(s)
- Rachel L Metras
- Virginia Institute of Autism, Charlottesville, VA, USA.
- Department of Curriculum, Instruction, & Special Education, University of Virginia, Charlottesville, VA, USA.
| | - Gregory P Hanley
- Department of Psychology, Western New England University, Springfield, MA, USA
- FTF Behavioral Consulting, Worcester, MA, USA
| | - Matthew J Carbone
- Department of Psychology, Western New England University, Springfield, MA, USA
- FTF Behavioral Consulting, Worcester, MA, USA
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41
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Hao X, Chen J, Tan R, Ma L, Pan J. Molecular characterization and functional analysis of glutathione S-transferase genes of pine wood nematode (Bursaphelenchus xylophilus) for avermectin. Comp Biochem Physiol C Toxicol Pharmacol 2023:109687. [PMID: 37331545 DOI: 10.1016/j.cbpc.2023.109687] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/11/2023] [Accepted: 06/13/2023] [Indexed: 06/20/2023]
Abstract
Pine wilt disease (PWD), caused by Bursaphelenchus xylophilus (pine wood nematodes, PWNs), is a forest disease that seriously threatens the health of Pinus forestry. Glutathione S-transferases (GSTs) play important roles in xenobiotic metabolism, lipophilic compound transport, antioxidative stress reactions, anti-mutagenesis, and antitumor activity. The analysis and investigation of the specific functions of GSTs in the metabolism of toxic substances in nematodes are important for identifying potential target genes to control the spread and transmission of B. xylophilus. In this study, 51 Bx-GSTs were found in the genome of B. xylophilus. Two key Bx-gsts (Bx-gst12 and Bx-gst40) were analyzed when B. xylophilus was exposed to avermectin. The expression of Bx-gst12 and Bx-gst40 was significantly increased when B. xylophilus was exposed to 1.6 and 3.0 mg/mL avermectin solutions. Notably, combined silencing of both Bx-gst12 and Bx-gst40 did not further increase the mortality rates under avermectin exposure. Mortality rates were significantly increased in nematodes treated with dsRNA compared to control nematodes (p < 0.05) after RNAi. The feeding ability of nematodes was also significantly reduced after treatment with dsRNA. These results suggested that Bx-gsts are associated with the detoxification process and feeding behavior of B. xylophilus. Silencing Bx-gsts leads to increased susceptibility to nematicides and reduces the feeding ability of B. xylophilus. Therefore, Bx-gsts will be a new control target of PWNs in the future.
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Affiliation(s)
- Xin Hao
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Jie Chen
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Ruina Tan
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Ling Ma
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Jialiang Pan
- Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang 110034, China.
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42
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Muhammad MA, Ahmad N, Akhter M, Rashid N. Structural and functional analyses of Pcal_0917, an α-glucosidase from hyperthermophilic archaeon Pyrobaculum calidifontis. Int J Biol Macromol 2023:125446. [PMID: 37330102 DOI: 10.1016/j.ijbiomac.2023.125446] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/16/2023] [Accepted: 06/14/2023] [Indexed: 06/19/2023]
Abstract
Genome analysis of Pyrobaculum calidifontis revealed the presence of α-glucosidase (Pcal_0917) gene. Structural analysis affirmed the presence of signature sequences of Type II α-glucosidases in Pcal_0917. We have heterologously expressed the gene and produced recombinant Pcal_0917 in Escherichia coli. Biochemical characteristics of the recombinant enzyme resembled to that of Type I α-glucosidases, instead of Type II. Recombinant Pcal_0917 existed in a tetrameric form in solution and displayed highest activity at 95 °C and pH 6.0, independent of any metal ions. A short heat-treatment at 90 °C resulted in a 35 % increase in enzyme activity. A slight structural shift was observed by CD spectrometry at this temperature. Half-life of the enzyme was >7 h at 90 °C. Pcal_0917 exhibited apparent Vmax values of 1190 ± 5 and 3.9 ± 0.1 U/mg against p-nitrophenyl α-D-glucopyranoside and maltose, respectively. To the best of our knowledge, Pcal_0917 displayed the highest ever reported p-nitrophenyl α-D-glucopyranosidase activity among the characterized counterparts. Moreover, Pcal_0917 displayed transglycosylation activity in addition to α-glucosidase activity. Furthermore, in combination with α-amylase, Pcal_0917 was capable of producing glucose syrup from starch with >40 % glucose content. These properties make Pcal_0917 a potential candidate for starch hydrolyzing industry.
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Affiliation(s)
- Majida Atta Muhammad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Nasir Ahmad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Mohsina Akhter
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan.
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Zhu J, Du D, Li Y, Zhang Y, Hu WL, Chen L, He X, Xia L, Mo X, Xie F, Luo C. Isolation of three MiDi19-4 genes from mango, the ectopic expression of which confers early flowering and enhances stress tolerance in transgenic Arabidopsis. Planta 2023; 258:14. [PMID: 37310483 DOI: 10.1007/s00425-023-04172-6] [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] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 06/01/2023] [Indexed: 06/14/2023]
Abstract
MAIN CONCLUSION Three Di19-4 genes were identified in mango. Overexpression of MiDi19-4B in A. thaliana promoted earlier flowering and enhanced drought, salt, and ABA resistance. Drought-induced protein 19 (Di19) is a drought-induced protein that is mainly involved in multiple stress responses. Here, three Di19-4 genes (MiDi19-4A/B/C) in mango (Mangifera indica L.) were identified, and the coding sequences (CDS) had lengths of 684, 666, and 672 bp and encoded proteins with 228, 222, and 224 amino acids, respectively. The promoters of the MiDi19-4 genes contained phytohormone-, light-, and abiotic stress-responsive elements. The MiDi19-4 genes were expressed in every tissue and highly expressed in leaves. Moreover, MiDi19-4 genes were highly correlated with the vegetative growth period and induced by polyethylene glycol (PEG) or salt stress. MiDi19-4B displayed the highest expression during the vegetative growth period and then showed decreased expression, and MiDi19-4B was highly expressed at both the late stage of the vegetative growth period and the initial stage of the flowering induction period. The 35S::GFP-MiDi19-4B fusion protein was located in the cell nucleus. The transgenic plants ectopically expressing MiDi19-4B exhibited earlier flowering and increased expression patterns of FRUITFULL (AtFUL), APETALA1 (AtAP1), and FLOWERING LOCUS T (AtFT). The drought and salt tolerance of MiDi19-4B transgenic plants was significantly increased, and these plants showed decreased sensitivity to abscisic acid (ABA) and considerably increased expression levels of drought- and salt-related genes and ABA signalling pathway genes. Additionally, bimolecular fluorescence complementation (BiFC) experiments revealed that the MiDi19-4B protein interacted with CAULIFLOWER (MiCAL1), MiCAL2, MiAP1-1, and MiAP1-2. Taken together, these results highlighted the important regulatory roles of MiDi19-4B in tolerance to multiple abiotic stresses and in flowering.
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Affiliation(s)
- Jiawei Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Daiyan Du
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Yuze Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Yili Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Wan Li Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Linghe Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Xinhua He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China.
| | - Liming Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Xiao Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Fangfang Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Cong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesGuangxi Key Laboratory for Agro-Environment and Agro-Product Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China.
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Schleifer-Katz E, Ortu D. Crafting Sequences of Sight and Sound: A Behavior Analysis of Filmmaking. Anal Verbal Behav 2023; 39:99-117. [PMID: 37397131 PMCID: PMC10313603 DOI: 10.1007/s40616-022-00178-5] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2022] [Indexed: 12/15/2022] Open
Abstract
The discipline of film studies often engages in analyses of the functions of filmmakers' decisions in terms of their effects on viewers. Behavior analysis uses a similar, functional-analytic approach toward understanding the relationship between individuals' behavior and the environmental effects that maintain their behavior. Given converging similarities between the two disciplines, a functional analysis of filmmaking is provided, using Skinner (1957)'s Verbal Behavior as a guiding framework. Similar to behavioral conceptualizations of language and speaker-listener verbal episodes, the analysis prioritizes functional explanation of the controlling variables and conditions that underlie the meaning of filmmakers' behavior and behavioral products, rather than solely focusing on their topographical description. Viewers' responses to the audiovisual stimuli of the film are emphasized as key controlling variables, through rules specifying contingency relations as well as through contingency shaping, including when the filmmaker acts as a self-viewer who directly shapes their own behavior. Their responding as a self-viewer during the production and editing of a film is explored as a problem-solving process, similar to other artists who serve as their own audience when creating and editing their behavioral products.
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Affiliation(s)
- Evan Schleifer-Katz
- Department of Behavior Analysis, University of North Texas, 1155 Union Circle #310919, Denton, TX 76203 USA
| | - Daniele Ortu
- Department of Behavior Analysis, University of North Texas, 1155 Union Circle #310919, Denton, TX 76203 USA
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45
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Huang X, Wang J, Xia L, Chen C, Wang M, Lu J, Lu T, Li K, Liang R, He X, Luo C. Functional studies of four MiFPF genes in mango revealed their function in promoting flowering in transgenic Arabidopsis. J Plant Physiol 2023; 285:153994. [PMID: 37105044 DOI: 10.1016/j.jplph.2023.153994] [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] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/19/2023] [Accepted: 04/20/2023] [Indexed: 05/22/2023]
Abstract
Flowering promoting factor (FPF) genes play a substantial regulatory role in the process of flowering. In the present study, four MiFPF genes, namely, MiFPF1, MiFPF2, MiFPF3a, and MiFPF3b, were obtained from mango (Mangifera indica L.). Tissue expression analysis showed that MiFPFs were expressed in all mango tissues. Specifically, MiFPF1 and MiFPF2 were highly expressed in leaves, while MiFPF3a and MiFPF3b were highly expressed in flowers and buds. The four MiFPF proteins localize to the nucleus. Overexpression of MiFPFs in transgenic Arabidopsis resulted in early flowering and upregulated the expression of APETAL1 (AP1), FLOWERING LOCUS D (FD) and FLOWERING LOCUS T (FT). MiFPF genes increased the root growth of transgenic Arabidopsis plants under gibberellin treatment. BiFC assays showed that MiFPFs can interact with several DELLA proteins. Taken together, our results demonstrate that the MiFPF gene was involved not only in promoting flowering but also in increasing root growth under gibberellin (GA3) treatment.
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Affiliation(s)
- Xing Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Jingzun Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Liming Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Canni Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Meng Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Jiamei Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Tingting Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Kaijiang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Rongzhen Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Xinhua He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China.
| | - Cong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China.
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Sun YM, Gan LH, Peng F, Zhou XY, Chen QS, Liu FT, Tang YL, Wu P, Lu JY, Ge JJ, Yen TC, Zuo CT, Song B, Wu JJ, Wang J. Autosomal dominant Parkinson's disease caused by the recently identified LRRK2 N1437D mutation in a Chinese family: Clinical features, imaging findings, and functional impact. Parkinsonism Relat Disord 2023; 111:105441. [PMID: 37201327 DOI: 10.1016/j.parkreldis.2023.105441] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 05/04/2023] [Accepted: 05/07/2023] [Indexed: 05/20/2023]
Abstract
INTRODUCTION Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common genetic cause of autosomal dominantly inherited Parkinson's disease (PD). Recently, a novel pathogenic variant (N1437D; c.4309A > G; NM_98578) in the LRRK2 gene has been identified in three Chinese families with PD. In this study, we describe a Chinese family with autosomal dominant PD that segregated with the N1437D mutation. A detailed clinical and neuroimaging characterization of the affected family members is reported. We also sought to investigate the functional mechanisms by which the detected mutation could cause PD. METHODS We characterized the clinical and imaging phenotype of a Chinese pedigree with autosomal dominant PD. We searched for a disease-causing mutation by targeted sequencing and multiple ligation-dependent probe amplification. The functional impact of the mutation was investigated in terms of LRRK2 kinase activity, guanosine triphosphate (GTP) binding, and guanosine triphosphatase (GTPase) activity. RESULTS The disease was found to co-segregate with the LRRK2 N1437D mutation. Patients in the pedigree exhibited typical parkinsonism (age at onset: 54.0 ± 5.9 years). One affected family member - who had evidence of abnormal tau accumulation in the occipital lobe on tau PET imaging - developed PD dementia at follow-up. The mutation markedly increased LRRK2 kinase activity and promoted GTP binding, without affecting GTPase activity. CONCLUSIONS This study describes the functional impact of a recently identified LRRK2 mutation, N1437D, that causes autosomal dominant PD in the Chinese population. Further research is necessary to investigate the contribution of this mutation to PD in multiple Asian populations.
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Affiliation(s)
- Yi-Min Sun
- Department of Neurology and National Research Center for Aging and Medicine & National Center for Neurological Disorders, State Key Laboratory of Medical Neurobiology, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Lin-Hua Gan
- Department of Neurology and National Research Center for Aging and Medicine & National Center for Neurological Disorders, State Key Laboratory of Medical Neurobiology, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Fang Peng
- Department of Neurology and National Research Center for Aging and Medicine & National Center for Neurological Disorders, State Key Laboratory of Medical Neurobiology, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Xin-Yue Zhou
- Department of Neurology and National Research Center for Aging and Medicine & National Center for Neurological Disorders, State Key Laboratory of Medical Neurobiology, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Qi-Si Chen
- Department of Neurology and National Research Center for Aging and Medicine & National Center for Neurological Disorders, State Key Laboratory of Medical Neurobiology, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Feng-Tao Liu
- Department of Neurology and National Research Center for Aging and Medicine & National Center for Neurological Disorders, State Key Laboratory of Medical Neurobiology, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Yi-Lin Tang
- Department of Neurology and National Research Center for Aging and Medicine & National Center for Neurological Disorders, State Key Laboratory of Medical Neurobiology, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Ping Wu
- PET Center and National Research Center for Aging and Medicine & National Center for Neurological Disorders, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Jia-Ying Lu
- PET Center and National Research Center for Aging and Medicine & National Center for Neurological Disorders, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Jing-Jie Ge
- PET Center and National Research Center for Aging and Medicine & National Center for Neurological Disorders, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | | | - Chuan-Tao Zuo
- PET Center and National Research Center for Aging and Medicine & National Center for Neurological Disorders, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Bin Song
- Department of Neurosurgery, Huashan Hospital, State Key Laboratory of Medical Neurobiology, Institute for Translational Brain Research, MOE Frontiers Center for Brain Science, Fudan University, 138 Medical College road, Shanghai, 200032, China.
| | - Jian-Jun Wu
- Department of Neurology and National Research Center for Aging and Medicine & National Center for Neurological Disorders, State Key Laboratory of Medical Neurobiology, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China.
| | - Jian Wang
- Department of Neurology and National Research Center for Aging and Medicine & National Center for Neurological Disorders, State Key Laboratory of Medical Neurobiology, Huashan Hospital, Fudan University, 12 Wulumuqi Zhong Road, Shanghai, 200040, China.
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Zhou H, Yan R, He H, Wei X, Liu S, Guo B, Zhang Y, Liu X, Rahman SU, Zhou C, He Z. Transcriptional profiling of long noncoding RNAs associated with flower color formation in Ipomoea nil. Planta 2023; 258:6. [PMID: 37219701 DOI: 10.1007/s00425-023-04142-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023]
Abstract
MAIN CONCLUSION LncRNAs regulate flower color formation in Ipomoea nil via vacuolar pH, TCA cycle, and oxidative phosphorylation pathways. The significance of long noncoding RNA (lncRNA) in diverse biological processes is crucial in plant kingdoms. Although study on lncRNAs has been extensive in mammals and model plants, lncRNAs have not been identified in Ipomoea nil (I. nil). In this study, we employed whole transcriptome strand-specific RNA sequencing to identify 11,203 expressed lncRNA candidates, including 961 known lncRNA and 10,242 novel lncRNA in the I. nil genome. These lncRNAs in I. nil had fewer exons and were generally shorter in length compared to mRNA genes. Totally, 1141 different expression lncRNAs (DELs) were significantly identified between white and red flowers. The functional analysis indicated that lncRNA-targeted genes were enriched in the TCA cycle, photosynthesis, and oxidative phosphorylation-related pathway, which was also found in differentially expressed genes (DEGs) functional enrichments. LncRNAs can regulate transcriptional levels through cis- or trans-acting mechanisms. LncRNA cis-targeted genes were significantly enriched in potassium and lysosome. For trans-lncRNA, two energy metabolism pathways, TCA cycles and oxidative phosphorylation, were identified from positive association pairs of trans-lncRNA and mRNA. This research advances our understanding of lncRNAs and their role in flower color development, providing valuable insights for future selective breeding of I. nil.
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Affiliation(s)
- Hanlin Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, China Three Gorges University, Yichang, 443002, China
| | - Ruizhi Yan
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, China Three Gorges University, Yichang, 443002, China
| | - Huan He
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, China Three Gorges University, Yichang, 443002, China
| | - Xinlin Wei
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, China Three Gorges University, Yichang, 443002, China
| | - Shuangcheng Liu
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, China Three Gorges University, Yichang, 443002, China
| | - Bintao Guo
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, China Three Gorges University, Yichang, 443002, China
| | - Yonghong Zhang
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, School of Basic Medicine, Biomedical Research Institute, Hubei University of Medicine, Shiyan, 442000, China
| | - Xiaoyun Liu
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, 430056, China
| | - Shafeeq Ur Rahman
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Chao Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, China Three Gorges University, Yichang, 443002, China.
| | - Zhengquan He
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, China Three Gorges University, Yichang, 443002, China.
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Luiz FN, Passarini MRZ, Magrini FE, Gaio J, Somer JG, Meyer RF, Paesi S. Metataxonomic characterization of the microbial community involved in the production of biogas with microcrystalline cellulose in pilot and laboratory scale. World J Microbiol Biotechnol 2023; 39:184. [PMID: 37147463 DOI: 10.1007/s11274-023-03573-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/08/2023] [Indexed: 05/07/2023]
Abstract
Biogas, produced in anaerobic digestion, is a sustainable alternative for generating energy from agro-industrial and municipal waste. Information from the microbiota active in the process expands the possibilities for technological innovation. In this study, taxonomic annotations, and functional prediction of the microbial community of the inoculum of two processes were carried out: an industrial unit (pilot-scale urban solid waste plant-IU) and a laboratory-scale reactor fed with swine and cattle waste (LS). The biochemical potential of biogas was obtained using tested inoculum with microcrystalline cellulose, obtaining 682 LN/kgVS (LSC-laboratory scale inoculum and microcrystalline cellulose), and 583 LN/kgVS (IUC-industrial unit inoculum and microcrystalline cellulose), which is equivalent to a recovery of 91.5% of total biogas to LSC. The phyla Synergistota and Firmicutes were more abundant in LS/LSC. In the IU/IUC (treatment of restaurant waste and customs seizures), there was a greater microbiological variety and a predominance of the Bacteroidota, Cloacimonadota, Firmicutes and Caldatribacteriota. The genus Methanosaeta predominated in the process, and it was possible to infer the genes (K01895, K00193 and K00625) related to acetoclastic pathway, as well as endoglucanases that are involved in the metabolism of cellulose (LSC). Terpenoids, polyketides, cofactors, and vitamin metabolism were higher in reactors that received different substrates (IU; IUC). The taxonomic and functional differences revealed the importance of determining the microbiota in the analysis of the potential of an inoculum, combined with the use of microcrystalline cellulose, which can provide optimization information in the production of clean energy.
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Affiliation(s)
- Franciele Natividade Luiz
- International Center of Renewable Energy (CIBIOGAS-ER)-Itaipu, Foz do Iguaçu, PR, Brazil
- Federal University of Latin American Integration (UNILA)-Environmental Biotechnology Laboratory, Foz do Iguaçu, PR, Brazil
| | | | - Flaviane Eva Magrini
- Molecular Diagnostic Laboratory, Biotechnology Institute, University of Caxias Do Sul (UCS), Caxias do Sul, RS, 95070-560, Brazil
| | - Juliano Gaio
- Molecular Diagnostic Laboratory, Biotechnology Institute, University of Caxias Do Sul (UCS), Caxias do Sul, RS, 95070-560, Brazil
| | - Juliana Gaio Somer
- International Center of Renewable Energy (CIBIOGAS-ER)-Itaipu, Foz do Iguaçu, PR, Brazil
- Federal University of Latin American Integration (UNILA)-Environmental Biotechnology Laboratory, Foz do Iguaçu, PR, Brazil
| | - Rafaela Faust Meyer
- International Center of Renewable Energy (CIBIOGAS-ER)-Itaipu, Foz do Iguaçu, PR, Brazil
- Federal University of Latin American Integration (UNILA)-Environmental Biotechnology Laboratory, Foz do Iguaçu, PR, Brazil
| | - Suelen Paesi
- Molecular Diagnostic Laboratory, Biotechnology Institute, University of Caxias Do Sul (UCS), Caxias do Sul, RS, 95070-560, Brazil.
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Wu Y, Zhang J, Li C, Deng X, Wang T, Dong L. Genome-wide analysis of TCP transcription factor family in sunflower and identification of HaTCP1 involved in the regulation of shoot branching. BMC Plant Biol 2023; 23:222. [PMID: 37101166 PMCID: PMC10134548 DOI: 10.1186/s12870-023-04211-0] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/03/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Sunflower is an important ornamental plant, which can be used for fresh cut flowers and potted plants. Plant architecture regulation is an important agronomic operation in its cultivation and production. As an important aspect of plant architecture formation, shoot branching has become an important research direction of sunflower. RESULTS TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors are essential in regulating various development process. However, the role of TCPs in sunflowers has not yet been studied. This study, 34 HaTCP genes were identified and classified into three subfamilies based on the conservative domain and phylogenetic analysis. Most of the HaTCPs in the same subfamily displayed similar gene and motif structures. Promoter sequence analysis has demonstrated the presence of multiple stress and hormone-related cis-elements in the HaTCP family. Expression patterns of HaTCPs revealed several HaTCP genes expressed highest in buds and could respond to decapitation. Subcellular localization analysis showed that HaTCP1 was located in the nucleus. Paclobutrazol (PAC) and 1-naphthylphthalamic acid (NPA) administration significantly delayed the formation of axillary buds after decapitation, and this suppression was partially accomplished by enhancing the expression of HaTCP1. Furthermore, HaTCP1 overexpressed in Arabidopsis caused a significant decrease in branch number, indicating that HaTCP1 played a key role in negatively regulating sunflower branching. CONCLUSIONS This study not only provided the systematic analysis for the HaTCP members, including classification, conserved domain and gene structure, expansion pattern of different tissues or after decapitation. But also studied the expression, subcellular localization and function of HaTCP1. These findings could lay a critical foundation for further exploring the functions of HaTCPs.
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Affiliation(s)
- Yu Wu
- College of Horticulture, Anhui Agricultural University, Changjiang Road, Hefei, 230036, Anhui, China
| | - Jianbin Zhang
- College of Horticulture, Anhui Agricultural University, Changjiang Road, Hefei, 230036, Anhui, China
| | - Chaoqun Li
- College of Horticulture, Anhui Agricultural University, Changjiang Road, Hefei, 230036, Anhui, China
| | - Xinyi Deng
- College of Horticulture, Anhui Agricultural University, Changjiang Road, Hefei, 230036, Anhui, China
| | - Tian Wang
- College of Horticulture, Anhui Agricultural University, Changjiang Road, Hefei, 230036, Anhui, China
| | - Lili Dong
- College of Horticulture, Anhui Agricultural University, Changjiang Road, Hefei, 230036, Anhui, China.
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Dai W, Liu R, Yang F, He G, Wei C. Denitrifying bacteria agent together with composite materials enhanced soil chemical properties and denitrifying functions in rare earth tailings: A field study. J Hazard Mater 2023; 448:130913. [PMID: 36758437 DOI: 10.1016/j.jhazmat.2023.130913] [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: 09/30/2022] [Revised: 01/23/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
The exploitation of ionic rare earth ore using ammonium sulfate extractant in China caused serious soil degradation and nitrogen compounds pollution in surrounding water. It was critical to improve soil properties and eliminate the nitrogen compounds and prevent their diffusion from the rare earth tailings. Here, we addressed this issue by conducting a field experiment for six months through four different treatments including control (CK), denitrifying bacteria agent mainly consisted of Bacillus (DBA), composite materials (CM) and denitrifying bacteria agent together with composite materials (DBA+CM). Besides, the treatments except CK were also amended with basic soil conditioners. DBA+CM could significantly increase soil pH from 5.01 to 6.84 (p ≤ 0.05). Cation exchange capacity in DBA+CM increased from below detection limit to 2.79 cmol+/kg. DBA+CM possessed the highest removal rate of soil NH4+ (95.14 %) and soil NO3- (66.46 %). Compared to CK, DBA+CM significantly increased the absolute abundance of nirS genes and relative abundance of denitrification, nitrate respiration, and nitrite respiration the most (p ≤ 0.05). Denitrification, nitrate respiration and nirS genes were negatively correlated with soil NO3- (p ≤ 0.05). This study demonstrates denitrifying bacteria agent together with composite materials can be a promising approach to control the pollution of nitrogen compounds in ionic rare earth tailings.
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Affiliation(s)
- Weijie Dai
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Renlu Liu
- School of Life Sciences, Key Laboratory of Agricultural Environmental Pollution Prevention and Control in Red Soil Hilly Region of Jiangxi Province, Jinggangshan University, Jian 343009, China
| | - Fen Yang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Genhe He
- School of Life Sciences, Key Laboratory of Agricultural Environmental Pollution Prevention and Control in Red Soil Hilly Region of Jiangxi Province, Jinggangshan University, Jian 343009, China.
| | - Chaoyang Wei
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.
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