Article
Biochemistry & Molecular Biology
Bowei Jia, Yan Wang, Dajian Zhang, Wanhong Li, Hongli Cui, Jun Jin, Xiaoxi Cai, Yang Shen, Shengyang Wu, Yongxia Guo, Mingzhe Sun, Xiaoli Sun
Summary: In this study, 16 GmCHYR genes with conserved Zinc_ribbon, CHY zinc finger and Ring finger domains were identified and divided into three groups. Additional 2-3 hemerythrin domains were found in the N terminus of Group III. Gene expression analysis revealed unique expression patterns in different soybean tissues/organs and under various abiotic stresses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Caio Canella Vieira, Jing Zhou, Diego Jarquin, Jianfeng Zhou, Brian Diers, Dean E. Riechers, Henry T. Nguyen, Grover Shannon
Summary: This study aimed to detect novel marker-trait associations and expand on previously identified genomic regions related to soybean response to off-target dicamba. Through genotyping and prediction models, eight genomic regions associated with off-target dicamba tolerance were identified, as well as candidate genes related to herbicide detoxification in plants.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Yueqiong Zhou, Liangliang He, Shaoli Zhou, Qing Wu, Xuan Zhou, Yawen Mao, Baolin Zhao, Dongfa Wang, Weiyue Zhao, Ruoruo Wang, Huabin Hu, Jianghua Chen
Summary: In this study, a total of 35 VLN genes were characterized from soybean and five related legumes. These genes were categorized into three groups based on phylogenetic relationships. Detailed analysis of the soybean VLNs revealed their distribution on 10 of the 20 chromosomes, as well as high group specificities in gene structures and protein motifs. Expression pattern analysis indicated widespread expression of most GmVLNs in various tissues, with three genes showing high expression levels in seeds. Moreover, the promoters of GmVLNs were found to be enriched with cis-elements related to abiotic stresses, hormone signals, and developmental processes, with the largest number associated with light responses.
Article
Plant Sciences
Xiangbo Duan, Ke Zhang, Huizi Duanmu, Yang Yu
Summary: In this study, the CRF gene family in soybean was analyzed using a genome-wide approach. A total of 26 members were identified and their sequence information, gene duplication, phylogenetic relationships, protein motifs, and gene structure were analyzed. The expression patterns of these CRFs in different tissues/organs and various environments were also investigated. The results showed spatial diversity in expression and differential response to cold, drought, and salt stress in soybean CRFs. This research provides valuable insights and information for future functional analysis of the CRF gene family in soybean.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Plant Sciences
Hong-Ru Xu, Ying Liu, Tai-Fei Yu, Ze-Hao Hou, Jia-Cheng Zheng, Jun Chen, Yong-Bin Zhou, Ming Chen, Jin-Dong Fu, You-Zhi Ma, Wen-Liang Wei, Zhao-Shi Xu
Summary: This study analyzed the distribution of TLP genes in the soybean genome and conducted phylogenetic analysis and protein modeling. It revealed the differential expression of GmTLPs under abiotic stresses and identified the important role of GmTLP8 in soybean drought and salt stress responses.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Liang Wang, Xinyu Yang, Yingqi Gao, Shouping Yang
Summary: The study identified 68 Glycine max TALE (GmTALE) superfamily members and classified them into BEL1-like and KNOX subfamilies. The gene structures showed similarities within the same subfamily or clade, with coding proteins exhibiting analogous motif and conserved domain compositions. Synteny analyses and evolutionary constraint evaluations provided insights into the evolution of GmTALE superfamily.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Yongwang Sun, Deying Wang, Mengmeng Shi, Yujie Gong, Shuwen Yin, Yexuan Jiao, Shangjing Guo
Summary: In this study, the ADF gene family and encoded proteins in soybean were systematically investigated. It was found that 18 GmADF genes were identified and mapped to different chromosomes. Phylogenetic analysis classified them into four groups and analysis of expression profiles showed their diverse response to abiotic stresses.
FRONTIERS IN PLANT SCIENCE
(2023)
Review
Plant Sciences
Rashmi Yadav, Sanjay Kalia, Parimalan Rangan, K. Pradheep, Govind Pratap Rao, Vikender Kaur, Renu Pandey, Vandna Rai, Celia Chalam Vasimalla, Sapna Langyan, Sanjula Sharma, Boopathi Thangavel, Virendra Singh Rana, Harinder Vishwakarma, Anshuman Shah, Abhishek Saxena, Ashok Kumar, Kuldeep Singh, Kadambot H. M. Siddique
Summary: Climate change poses challenges to the oilseed industry, particularly sesame cultivation, but research on enhancing genetics, improving quality, and understanding stress tolerance mechanisms in sesame is lacking. This study highlights the challenges faced by farmers and researchers in sesame cultivation and suggests potential genetic and genomic resources for developing tolerant varieties and improving production under changing climatic conditions, including exploring beneficial agro-morphological traits and utilizing wild relatives for hybridization.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Binhui Guo, Jianhua Zhang, Chunhong Yang, Lu Dong, Heng Ye, Babu Valliyodan, Henry T. Nguyen, Li Song
Summary: In this research, a genome-wide survey was conducted to identify and classify the LEA genes in soybean. The study characterized the GmLEAs by determining their subcellular localization, gene duplication, structure, motif conservation, and tissue expression pattern. The expression profile analysis revealed that certain GmLEAs respond to drought and salt stress. Additionally, the study explored the function of GmLEA4_19 and found that it enhances drought tolerance in Arabidopsis and soybean. These findings contribute to a better understanding of the biological roles of LEA genes in soybean.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Xiaofei Ma, Wenying Xu, Tong Liu, Ruying Chen, Hong Zhu, Huiying Zhang, Chunmei Cai, Shuai Li
Summary: In this study, 54 GmDIR genes were identified and characterized in soybean, most of which contained a single exon gene structure and were grouped into four subfamilies. Differences in the cis-acting elements in the GmDIR promoter regions may lead to distinct expression patterns of GmDIRs in different tissues.
Article
Biochemistry & Molecular Biology
Mohsen Yoosefzadeh-Najafabadi, Milad Eskandari, Sepideh Torabi, Davoud Torkamaneh, Dan Tulpan, Istvan Rajcan
Summary: A genome-wide association study (GWAS) is a recommended method for discovering marker-trait associations (MTAs) in plant species. This study evaluated the potential use of two machine learning algorithms (SVR and RF) in GWAS and compared them with two conventional methods (MLM and FarmCPU) for identifying MTAs for soybean-yield components. The results demonstrated the potential benefit of using SVR in GWAS for identifying MTAs with potential causal effects on target traits.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Chemistry, Organic
Mohamad Hesam Shahrajabian, Yue Kuang, Haoran Cui, Lan Fu, Wenli Sun
Summary: This article investigates the chemical compounds and metabolic changes of important medicinal plants in traditional Chinese medicine under abiotic and biotic stresses. Further research is needed to evaluate the effects of these stresses on active compounds in medicinal plants, and advanced techniques such as LC-MS, GC-MS, and NMR can provide a better understanding of the chemical components of these plants.
CURRENT ORGANIC CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Jun Liu, Jiming Zheng
Summary: This paper proposes a new method that utilizes multiple characteristics of nodes for evaluating their importance. The method includes the definition of an extended degree and the introduction of E-shell hierarchy decomposition. Based on these components, a hybrid characteristic centrality and its extended version are proposed. Experimental results show that the new approach outperforms the other five approaches in terms of accuracy and resolution.
SCIENTIFIC REPORTS
(2023)
Review
Biochemistry & Molecular Biology
Masoumeh Naserkheil, Zeinab Manzari, Chang Gwon Dang, Seung Soo Lee, Mi Na Park
Summary: The purpose of this review was to explore and summarize different studies on the detection and characterization of candidate genes and genomic regions associated with economically important traits in Hanwoo beef cattle. GWAS analysis identified several genes located on chromosomes 6 and 14 that are associated with carcass and growth traits in Hanwoo.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Cheng Liu, Xianlian Chen, Wubin Wang, Xinyang Hu, Wei Han, Qingyuan He, Hongyan Yang, Shihua Xiang, Junyi Gai
Summary: In this study, an improved wild soybean chromosome segment substitution line (CSSL) population, SojaCSSLP5, was developed, which was genotyped through whole-genome resequencing to identify genetic changes from wild soybean to cultivated soybean. Using the SNPLDB-map, several candidate genes related to seed-coat color and days to flowering were identified and verified, demonstrating the efficiency of the CSSL population in identifying candidate wild vs. cultivated gene-alleles. The integration of parental DNA and RNA sequencing data provided a reliable platform for further research on genetic changes between wild and cultivated soybean.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Jose Rafael da Silva Araujo, Juliana Vieira de Barros Arcoverde, Marilia Grasielly de Farias Silva, Edson Renan Barros de Santana, Persio Alexandre da Silva, Silvany Araujo de Sousa, Neide Santos, Pedro Marcos de Almeida, Claudia Sampaio de Andrade Lima, Ana Maria Benko-Iseppon, Rafael Jorge Santos Aracati Padilha, Marccus Alves, Ana Christina Brasileiro-Vidal
Summary: This study evaluated the biological potential of Amburana cearensis leaves and found that the ethyl acetate fraction showed the highest antioxidant activity. It also did not exhibit cytotoxicity or genotoxicity, indicating it as a safe natural antioxidant source.
DRUG AND CHEMICAL TOXICOLOGY
(2023)
Article
Agriculture, Dairy & Animal Science
Pabola S. Nascimento, Marcelo T. Moura, Roberta L. Oliveira-Silva, Pamela Ramos-Deus, Claudio C. Bartolomeu, Ana M. Benko-Iseppon, Jose C. Ferreira-Silva, Antonio S. Santos Filho, Marcos A. L. Oliveira
Summary: This study investigates the correlations between PATF gene expression patterns and mRNA regulatory features in sheep embryos. It identifies different PATF gene expression patterns and reveals their associations with mRNA 3'UTR length, polyadenylation sites, and m6A sites.
Article
Veterinary Sciences
Ludymila F. Cantanhede, Marcelo T. Moura, Roberta L. Oliveira-Silva, Pabola S. Nascimento, Jose C. Ferreira-Silva, Ana M. Benko-Iseppon, Marcos A. L. Oliveira
Summary: This study identified transcription factors involved in the regulation of oocyte in vitro maturation, with MYC as a core component of FSH signaling and THAP11 acting independently.
ACTA VETERINARIA HUNGARICA
(2022)
Article
Genetics & Heredity
Mitalle Karen da Silva Matos, Ana Maria Benko-Iseppon, Joao Pacifico Bezerra-Neto, Jose Ribamar Costa Ferreira-Neto, Yu Wang, Hai Liu, Valesca Pandolfi, Lidiane Lindinalva Barbosa Amorim, Lilia Willadino, Thialisson Caaci do Vale Amorim, Ederson Akio Kido, Rosana Pereira Vianello, Michael P. Timko, Ana Christina Brasileiro-Vidal
Summary: This study investigated the WRKY gene family in the drought-tolerant legume cowpea and identified key genes involved in the response to root dehydration stress. The findings provide a foundation for improving drought tolerance in this important crop.
Article
Plant Sciences
Jose Ribamar Costa Ferreira-Neto, Flavia Czekalski de Araujo, Roberta Lane de Oliveira Silva, Natoniel Franklin de Melo, Valesca Pandolfi, Gabriella Frosi, David Anderson de Lima Morais, Manasses Daniel da Silva, Rebeca Rivas, Mauro Guida Santos, Saulo de Tarso Aidar, Carolina Vianna Morgante, Ana Maria Benko-Iseppon
Summary: This study reveals the physiological, biochemical, and molecular mechanisms underlying the response of Stylosanthes scabra to water deficit and provides candidate genes for developing drought-tolerant crop varieties through biotechnological applications.
PHYSIOLOGIA PLANTARUM
(2022)
Article
Plant Sciences
Mayara C. B. S. Rocha, Sonia M. B. Pereira, Maria F. Oliveira-Carvalho, Ana M. Benko-Iseppon, Caroline F. Ximenes, Mutue T. Fujii, Valeria Cassano
Summary: This study evaluated the diversity of Udotea in northeastern Brazil using morphological-based taxonomy and plastid molecular markers. A new species, Udotea dotyi, was discovered in the western south Atlantic Ocean. Further studies are needed to define a taxon named as 'Udotea cyathiformis'.
Article
Biotechnology & Applied Microbiology
Leandro S. Velez, Flavia F. Aburjaile, Antonio R. G. Farias, Ana D. B. Baia, Willams J. Oliveira, Adriano M. F. Silva, Ana M. Benko-Iseppon, Vasco Azevedo, Bertram Brenig, Jong H. Ham, Elineide B. Souza, Marco A. S. Gama
Summary: Genomic approaches were used to study two putative novel lineages of Burkholderia cenocepacia found in the semi-arid region of north-east Brazil causing onion sour skin. Whole genome sequencing and taxogenomic analysis revealed that these strains represent two novel species of the Bcc, named Burkholderia semiarida sp. nov. and Burkholderia sola sp. nov. The strains CCRMBC74T and CCRMBC51T were proposed as the type strains for these species.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2023)
Article
Microbiology
Juan Carlos Ariute, Andrei Giachetto Felice, Siomar Soares, Marco Aurelio Siqueira da Gama, Elineide Barbosa de Souza, Vasco Azevedo, Bertram Brenig, Flavia Aburjaile, Ana Maria Benko-Iseppon
Summary: In this study, 14 Ralstonia solanacearum isolates from Brazil were sequenced and analyzed, revealing their similarity to R. solanacearum genomes in NCBI. The new isolates shared more Rips with Moko IIA and Moko IIB than with other public BW genome isolates from Brazil. These findings provide important insights into the association between Rips repertoire and host specificities.
Review
Infectious Diseases
Carlos Andre dos Santos-Silva, Jose Ribamar Costa Ferreira-Neto, Vinicius Costa Amador, Joao Pacifico Bezerra-Neto, Livia Maria Batista Vilela, Eliseu Binneck, Mireli de Santana Rego, Manasses Daniel da Silva, Ana Luiza Trajano Mangueira de Melo, Rahisa Helena da Silva, Ana Maria Benko-Iseppon
Summary: Non-specific lipid transfer proteins (nsLTPs) have diverse roles in plant molecular physiology and development, including protection against pathogens. These antimicrobial agents show remarkable efficacy against bacterial and fungal pathogens. The discovery of plant-originated, cysteine-rich antimicrobial peptides like nsLTPs has opened up possibilities for using these organisms as potential biofactories for synthesizing antimicrobial compounds.
Article
Biology
Artemisa Nazare Costa Borges-Martins, Jose Ribamar Costa Ferreira-Neto, Manasses Daniel da Silva, David Anderson de Lima Morais, Valesca Pandolfi, Roberta Lane de Oliveira Silva, Ana Luiza Trajano Mangueira de Melo, Antonio Felix da Costa, Ana Maria Benko-Iseppon
Summary: This study analyzed the conserved transcriptional signatures in cowpea genotypes resistant to cowpea viruses, and found that cowpea utilized generic mechanisms during its early interaction with the viruses and subsequently employed more specialized strategies. This work represents the first study investigating conserved mechanisms in the cowpea defense response to viral inoculations, highlighting relevant processes for initial defense responses.
Article
Parasitology
Samuel Ricarte de Aquino, Lucyo Flavio Bezerra Diniz, Savio Luiz Pereira Nunes, Roberta Lane de Oliveira Silva, Gisele Veneroni Gouveia, Joao Jose Simoni Gouveia, Kamila Gaudencio da Silva Sales, Filipe Dantas-Torres, Rodrigo Feliciano do Carmo
Summary: This study investigated the use of kDNA-based qPCR for monitoring parasite load in VL patients after treatment. The results showed a significant reduction in parasite load after treatment, although one patient experienced an increase in parasite load and relapse. These findings demonstrate the utility of kDNA-based qPCR for post-treatment follow-up in VL cases.
REVISTA DA SOCIEDADE BRASILEIRA DE MEDICINA TROPICAL
(2023)
Article
Biochemical Research Methods
Lethicia Souza Tavares, Roberta Lane Oliveira-Silva, Marcelo Tigre Moura, Jessica Barboza da Silva, Ana Maria Benko-Iseppon, Jose Vitor Lima-Filho
Summary: This study identified suitable reference genes for different conditions in a mouse model of Listeria monocytogenes and highlighted the importance of RT-qPCR in gene expression analysis.