Article
Plant Sciences
Rohit Bharati, Madhab Kumar Sen, Ram Kumar, Aayushi Gupta, Jana Ziarovska, Eloy Fernandez-Cusimamani, Olga Leuner
Summary: This study assessed the suitability of ten commonly used reference genes as optimal reference genes in M. officinalis under different abiotic stress conditions and plant organs. The combination of EF-1 alpha and GAPDH was recommended as the best reference genes for gene expression studies in M. officinalis.
Article
Biochemistry & Molecular Biology
Kathannan Sankar, Hyung Joo Yoon, Young Bo Lee, Kyeong Yong Lee
Summary: Bumble bees are important alternative pollinators and model insects. This study identified stable reference genes for the bumble bee species and their different lines and tissues using RT-qPCR procedures and four analysis programs. The results emphasized the need to evaluate the stability of candidate reference genes for any differently designed lines and tissue conditions in bumble bee species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Agronomy
Shengyi Bai, Xiaomin Wang, Meng Guo, Guoxin Cheng, Abid Khan, Wenkong Yao, Yanming Gao, Jianshe Li
Summary: This study screened out the most stable reference genes and studied the expression of related genes in the interaction between tomatoes and powdery mildew, providing a calibration basis for the expression of related functional genes.
Article
Agriculture, Dairy & Animal Science
Mingzhe Fu, Xiaolong Xu, Zefang Cheng, Junru Zhu, Ao Sun, Ganggang Xu, Xiaopeng An
Summary: This study analyzed the transcriptome and proteome of dairy goats infected with Corynebacterium pseudotuberculosis. The results showed that in the early stage of infection, dairy goats can defend against bacterial invasion through multiple pathways. However, in the later stages of infection, a few gene-protein pairs play a role in protein processing in the endoplasmic reticulum pathway. The mRNA and protein expressions of dairy goats indicate their adaptability to the bacteria, providing guidance for treatment and feeding management according to different periods of time.
Article
Biochemistry & Molecular Biology
Zhiwei Chen, Nigel G. Halford, Chenghong Liu
Summary: Real-time quantitative PCR is a technique for measuring the content of a specific nucleic acid sequence in a sample, and it can be divided into absolute and relative quantitative methods. Relative quantification is mainly used for gene expression in functional genomics and transcriptome studies. However, to accurately use this technology, key points such as designing specific primers, selecting appropriate reference genes, and performing scientific calculations and statistics are crucial. This article proposes a workflow for relative quantitative PCR and introduces relevant points to help beginners better understand and utilize this technology.
Article
Biochemistry & Molecular Biology
Mengdi Chen, Zhengbo Wang, Ziyuan Hao, Hongying Li, Qi Feng, Xue Yang, Xiaojiao Han, Xiping Zhao
Summary: This study selected suitable internal reference genes for studying gene expression in Broussonetia papyrifera under abiotic stresses. Through RT-qPCR and stability analysis, the best internal reference genes and their combinations were determined for different stress conditions and tissues. The reliability of the screened internal reference genes was further verified by analyzing the expression patterns of target genes. This study lays the foundation for functional analysis and regulatory mechanism research of genes in B. papyrifera.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Horticulture
Chenjie Zhang, Chengwei Song, Linfeng Chen, Huili Ma, Yabing Zhang, Dalong Guo, Lili Guo, Xiaogai Hou
Summary: The aim of this study was to identify suitable reference genes for normalizing the expression levels of miRNA in different developmental stages and tissues. Five algorithms were used for stability analysis, and the results identified mtr-MIR160b-p3 and gma-miR394a-5p as the most stable miRNAs during bud development in early-flowering tree peony 'Feng dan', while PC-5p-19095 was the most stable during bud development in late-flowering tree peony 'Lian he'. Additionally, mtr-miR159a was found to be the most stable miRNA during flower development stages of different tree peony varieties.
Article
Multidisciplinary Sciences
Xiujie Yin, Taotao He, Kun Yi, Yihang Zhao, Yao Hu, Jiaxue Liu, Xiaomeng Zhang, Lingdong Meng, Lina Wang, Haoyue Liu, Yonggang Li, Guowen Cui
Summary: Twelve reference genes were selected based on transcriptomic data for stable expression analysis in various organs of Caucasian clover under different stress conditions. Results showed that different reference genes were most stable under different stress conditions, with RCD1 and NLI2 identified as the most stable reference genes across all organs.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Saqib Rahman, Zhenzhen Zhao, Muhammad Umair Sial, Yanning Zhang, Hongyun Jiang
Summary: This study confirmed the stability of Actin and 18S as reference genes for normalizing the expression of target genes in Myzus persicae under different conditions. Both genes were effective in normalizing the expression levels of target genes under insecticide treatment and starvation. However, Actin was more stable than 18S at the developmental stages of M. persicae.
Article
Biochemical Research Methods
Jun Kawase, Tomotake Sakai, Masaaki Iwaki, Kaoru Umeda, Aiko Fukuma, Naoki Fujisawa, Yuta Kawakami, Hiroki Hayashi, Mieko Wada
Summary: A multiplex real-time PCR assay has been developed to rapidly discriminate Corynebacterium ulcerans from Corynebacterium pseudotuberculosis and detect the bacterial diphtheria toxin gene. This assay is a valuable tool for identification of potentially toxigenic C. ulcerans.
JOURNAL OF MICROBIOLOGICAL METHODS
(2022)
Article
Agriculture, Dairy & Animal Science
Ahmed Magdy Selim, Samar Magdy Atwa, Attia Abdullah El Gedawy, Emad Elsayed Younis
Summary: This study conducted the first phylogenetic analysis of C. pseudotuberculosis isolate in Egypt, showing high homology between the PLD gene isolate and strains from India, Sudan, etc. The findings provide valuable information on the molecular detection and phylogeny of C. pseudotuberculosis in Egypt, and could be beneficial for other CLA endemic countries with similar animal breeding practices.
ANIMAL BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Hao Zhan, Hanzhang Liu, Tianchong Wang, Lin Liu, Wanfeng Ai, Xiujun Lu
Summary: This study selected 11 candidate reference genes and evaluated their expression stability in different tissues and under various stress conditions in Quercus mongolica. The results showed that the most stable genes varied in different experimental environments. Moreover, the study demonstrated the reliability of the selected reference genes in different tissues and under different stress conditions.
Article
Biotechnology & Applied Microbiology
Jeongah Song, Jeonghee Cho, Jeongsik Park, Jeong Ho Hwang
Summary: This study identified stable reference genes in seven tissues across four developmental stages in minipigs, which can be used to evaluate mRNA expression levels. HPRT1 and 18S were found to be the most stable genes. The expression levels of ACE2 in the intestine and kidney increased significantly at PND28, consistent with the ACE2 expression pattern in humans.
Article
Ecology
Agnes Vallier, Elisa Dell'Aglio, Mariana Galvao Ferrarini, Ophelie Hurtado, Carole Vincent-Monegat, Abdelaziz Heddi, Rita Rebollo, Anna Zaidman-Remy
Summary: This study used transcriptomic high-throughput analysis to identify a subset of stably expressed genes from different developmental stages of the gut and associated-bacteriomes of Sitophilus oryzae, which can be used as reference genes in qRT-PCR experiments. Two genes, TAO and YTH3, were selected as suitable genes for comparing transcript abundance in symbiotic and aposymbiotic insects at various developmental stages. These well-conserved genes have the potential to be applied in other insect species, emphasizing the importance of using unbiased methods for reference gene selection.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Physiology
Jinrong Tang, Gemei Liang, Shaoqi Dong, Shuang Shan, Man Zhao, Xianru Guo
Summary: By evaluating the stability of reference genes in Athetis dissimilis under different conditions, suitable reference genes for different experimental conditions can be determined. Different reference genes are needed under different experimental conditions, providing a reliable basis for studying gene expression in A. dissimilis.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Genetics & Heredity
Hendor N. R. Jesus, Juliana N. N. Ramos, Danilo J. P. G. Rocha, Daniele A. A. Alves, Carolina S. S. Silva, Joao V. O. Cruz, Veronica V. Vieira, Cassius Souza, Louisy S. S. Santos, Jesus Navas, Rommel T. J. Ramos, Vasco Azevedo, Eric R. G. R. Aguiar, Ana L. L. Mattos-Guaraldi, Luis G. C. Pacheco
Summary: This study analyzed the genomes of C. striatum isolates and identified genomic characteristics that contribute to its pathogenicity and multidrug resistance. The research sheds light on the transition of C. striatum from a normal skin microbiome constituent to a multidrug-resistant and invasive pathogen.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2023)
Review
Multidisciplinary Sciences
Joyce Dutra, Rosimeire Gomes, Glen Jasper Yupanqui Garcia, Danitza Xiomara Romero-Cale, Mariana Santos Cardoso, Vinicius Waldow, Claudia Groposo, Rubens N. Akamine, Maira Sousa, Henrique Figueiredo, Vasco Azevedo, Aristoteles Goes-Neto
Summary: This systematic review evaluates the taxonomic composition and relative abundance of microorganisms associated with microbiologically influenced corrosion (MIC) in the oil and gas industry. The results indicate the presence of functional groups involved in MIC processes and the influence of environmental and human factors on microbial activity and metabolic patterns. The findings provide valuable insights for the development of standardized approaches to control MIC in oil and gas production and transport structures.
Article
Parasitology
Gabriela Merker Breyer, Bianca Fagundes Saggin, Silvia de Carli, Maria Eduarda Rocha Jacques da Silva, Mateus Matiuzzi da Costa, Bertram Brenig, Vasco Ariston de Carvalho Azevedo, Marisa Ribeiro de Itapema Cardoso, Franciele Maboni Siqueira
Summary: This study aims to uncover the virulence profile of Staphylococcus pseudintermedius strains from canine origin. MRSP and MSSP strains were compared to determine their clinical implications. The findings highlight the wide spread of highly virulent and drug-resistant strains, posing potential concerns for One Health issues.
Article
Biotechnology & Applied Microbiology
Jorge Luis Nicoleti, Erik Sobrinho Braga, Danijela Stanisic, Milka Jadranin, Debora Andrea Evangelista Facanha, Thiago Doria Barral, Samira Abdallah Hanna, Vasco Azevedo, Roberto Meyer, Ljubica Tasic, Ricardo Wagner Portela
Summary: This study performed a metabolomic study of Corynebacterium pseudotuberculosis infection in goats, revealing possible biomarkers for the disease. The results provide new avenues for the treatment, immunodiagnosis, and immunoprophylactic tools for caseous lymphadenitis (CLA).
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Microbiology
Juliana Lima Alves, Luisa Lemos, Nubia Morais Rodrigues, Vanessa Bastos Pereira, Patricia A. Vieira Barros, Maria Cecilia Campos Canesso, Mauro A. F. Guimaraes, Denise Carmona Cara, Anderson Miyoshi, Vasco Ariston Azevedo, Tatiani Uceli Maioli, Ana Cristina Gomes-Santos, Ana Maria Caetano Faria
Summary: Inflammatory bowel diseases (IBD) are gastrointestinal disorders characterized by a breakdown in intestinal homeostasis by inflammatory immune responses. Novel strategies for ameliorating IBD have been proposed. The study showed that different strains of Lactococcus lactis improved clinical scores and parameters of colitis, confirming their anti-inflammatory properties in this model.
BRAZILIAN JOURNAL OF MICROBIOLOGY
(2023)
Article
Cell Biology
Kenneth Lundstrom, Altijana Hromic-Jahjefendic, Esma Bilajac, Alaa A. A. Aljabali, Katarina Baralic, Nagwa A. Sabri, Eslam M. Shehata, Mohamed Raslan, Sara A. Raslan, Ana Claudia B. H. Ferreira, Lidiane Orlandi, Angel Serrano-Aroca, Vladimir N. Uversky, Sk. Sarif Hassan, Elrashdy M. Redwan, Vasco Azevedo, Khalid J. Alzahrani, Khalaf F. Alsharif, Ibrahim F. Halawani, Fuad M. Alzahrani, Murtaza M. Tambuwala, Debmalya Barh
Summary: The COVID-19 pandemic has led to extensive research and development of drugs and vaccines for SARS-CoV-2. Vaccines based on viral vectors, nucleic acids, and whole viral particles have been particularly successful and have received emergency authorization for global mass vaccination. However, emerging variants have raised concerns about vaccine efficacy.
CELLULAR SIGNALLING
(2023)
Article
Biology
Amanda de Oliveira Matos, Thais Cristina Vilela Rodrigues, Sandeep Tiwari, Pedro Henrique dos Santos Dantas, Geraldo Rodrigues Sartori, Vasco Ariston de Carvalho Azevedo, Joao Herminio Martins Da Silva, Siomar de Castro Soares, Marcelle Silva-Sales, Helioswilton Sales-Campos
Summary: Researchers developed a multi-epitope vaccine using immunoinformatics tools to prevent severe acute gastroenteritis caused by RV and NV. The vaccine contains multiple epitopes that are immunogenic and can induce a Th1 immune response, while being safe without allergenic or toxic regions.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Microbiology
Roselane Goncalves dos Santos, Raquel Hurtado, Diego Lucas Neres Rodrigues, Alessandra Lima, William Ferreira dos Anjos, Claudia Rifici, Anna Rita Attili, Sandeep Tiwari, Arun Kumar Jaiswal, Sharon J. Spier, Giuseppe Mazzullo, Francielly Morais-Rodrigues, Anne Cybelle Pinto Gomide, Luis Claudio Lima de Jesus, Flavia Figueira Aburjaile, Bertram Brenig, Vincenzo Cuteri, Thiago Luiz de Paula Castro, Nubia Seyffert, Anderson Santos, Aristoteles Goes-Neto, Thiago de Jesus Sousa, Vasco Azevedo
Summary: In this study, the classification of Dietzia strains was reevaluated through comparative genomics. It was found that some species were misclassified and could be reassigned into four distinct groups. Additionally, genomic plasticity analysis revealed differences in the presence or absence of symbiotic islands and pathogenic islands among the Dietzia strains. This research suggests that combining pan-genome analysis and phylogenomic approaches can be an alternative method for the classification and differentiation of new species in the genus Dietzia.
RESEARCH IN MICROBIOLOGY
(2023)
Article
Microbiology
Raquel Hurtado, Debmalya Barh, Luis Claudio Lima de Jesus, Marcus Vinicius Canario Viana, Sandeep Tiwari, Flavia Figueira Aburjaile, Dennis E. Carhuaricra Huaman, Bertram Brenig, Lenin Maturrano Hernandez, Vasco Azevedo
Summary: This study investigated the genomic diversity and antimicrobial resistance of Salmonella Typhimurium isolates from guinea pigs in Peru. The findings revealed different populations of isolates and common transmissible resistance plasmids in guinea pigs and human hosts.
RESEARCH IN MICROBIOLOGY
(2023)
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
Danitza Xiomara Romero-Calle, Francisnei Pedrosa-Silva, Luiz Marcelo Ribeiro Tome, Vagner Fonseca, Raquel Guimaraes Benevides, Leila Thaise Santana de Oliveira Santos, Tulio de Oliveira, Mateus Matiuzzi da Costa, Luiz Carlos Junior Alcantara, Vasco Ariston de Carvalho Azevedo, Bertram Brenig, Thiago M. Venancio, Craig Billington, Aristoteles Goes-Neto
Summary: Despite the use of new treatments, antimicrobial resistance is still increasing, calling for novel strategies. Bacteriophages have the potential to control bacterial pathogens like Salmonella. A Salmonella phage, Wara, was isolated from water samples in the Subae River Basin in Brazil. Its genome was sequenced using Oxford Nanopore Technologies and Illumina HiSeq, and assembly was carried out using Racon and Unicycler. Wara was found to be a member of the Tequintavirus genus and has therapeutic and biocontrol potential against Salmonella in healthcare and agriculture.
Article
Microbiology
Danielle Machado Pagani, Stefania P. R. Ventura, Duong Vu, Thairine Mendes-Pereira, Luiz Marcelo Ribeiro Tome, Daniel Santana de Carvalho, Diogo Henrique Costa-Rezende, Rodrigo Bentes Kato, Glen Jasper Yupanqui Garcia, Jozsef Geml, Vincent Robert, Ng Haig They, Bertram Brenig, Vasco Azevedo, Maria Lucia Scroferneker, Patricia Valente, Aristoteles Goes-Neto
Summary: Studies on the fungal communities in aquatic environments are relatively recent, especially in freshwater ecosystems. Human activities, such as effluent discharge, pose threats to these water bodies. This study found that the fungal diversity and specific operational taxonomic units (OTUs) were higher in ecotones, highlighting our limited understanding of subtropical freshwater mycobiota.
Review
Chemistry, Medicinal
Mohamed A. Raslan, Sara A. Raslan, Eslam M. Shehata, Amr S. Mahmoud, Kenneth Lundstrom, Debmalya Barh, Vasco Azevedo, Nagwa A. Sabri
Summary: Nutrigenomics studies the impact of diets or nutrients on gene expression and phenotypes through high-throughput technologies, such as transcriptomics, proteomics, and metabolomics. The bioactive components of diets and nutrients transmit information through altered gene expression, affecting the overall function and traits of an organism. Recent evidence suggests a correlation between gene regulation and antibiotic resistance in response to diets and nutrients, providing a potential alternative solution against antibiotic resistance. However, little progress has been made in this area.
Article
Biochemistry & Molecular Biology
Pedro Henrique Marques, Thais Cristina Vilela Rodrigues, Eduardo Horta Santos, Lucas Bleicher, Flavia Figueira Aburjaile, Flaviano S. Martins, Carlo Jose Freire Oliveira, Vasco Azevedo, Sandeep Tiwari, Siomar Soares
Summary: Researchers have developed a multi-epitope vaccine based on reverse vaccinology and immunoinformatics to combat vibriosis and cholera caused by pathogenic Vibrio spp. In silico analysis suggests that the vaccine is stable, soluble, non-toxic, and non-allergenic, and has the potential to elicit immune responses. However, further experimental analyses are required to evaluate its efficacy in vivo.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Food Science & Technology
Rodrigo Dias de Oliveira Carvalho, Houem Rabah, Juan Carlos Ariute, Flavia Figueira Aburjaile, Bertram Brenig, Eric Guedon, Yves Le Loir, Gwenael Jan, Vasco Azevedo
Summary: This study investigated the effects of two types of cheese fermented by probiotic bacteria on gut microbiota and metabolic pathways. The results showed that these cheeses did not disturb the microbial community ecology, but Emmental cheese increased the abundance of some beneficial bacteria. Furthermore, Emmental cheese may produce bioactive metabolites and cooperate with other commensal species to produce beneficial substances. Mice with colitis showed restored metabolic functions of the impaired microbiome when treated with a specific cheese.