Article
Agriculture, Dairy & Animal Science
Xiangchun Pan, Jiali Cai, Yifei Wang, Dantong Xu, Yao Jiang, Wentao Gong, Yuhan Tian, Qingpeng Shen, Zhe Zhang, Xiaolong Yuan, Jiaqi Li
Summary: This study provides a comprehensive analysis of gene expression in pigs and reveals the presence of housekeeping genes, tissue-specific genes, and co-expressed genes. The results offer a fresh perspective on the transcriptional regulation of pig tissues.
Article
Microbiology
Fernanda Terezinha Moura, Luisa Caroline Ferraz Helene, Renan Augusto Ribeiro, Marco Antonio Nogueira, Mariangela Hungria
Summary: This study identified 13 strains of potential new Rhizobium species isolated from common bean nodules in Brazil. Further characterization confirmed the phylogenetic allocation and revealed five new species. These new strains exhibited different characteristics in terms of nodulation and symbiotic features.
ARCHIVES OF MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
H. Shin, R. E. Morty, J. M. Sucre, N. M. Negretti, M. Markmann, H. Hossain, S. Krauss-Etschmann, S. Dehmel, A. Hilgendorff
Summary: This study evaluated candidate genes as reference genes for the developing mouse lung, taking into consideration biological, technical, and experimental conditions. By analyzing publicly available microarray datasets and using RT-qPCR and single-cell RNA-sequencing, we identified stable and reliable reference genes for different conditions.
SCIENTIFIC REPORTS
(2022)
Article
Plant Sciences
Junjie Zhang, Yufeng Feng, Jingqi Wang, Entao Wang, Mitchell Andrews
Summary: By using PCR-RFLP of IGS sequences and sequence analyses of various genes, this study identified diverse Bradyrhizobium species and a novel Bradyrhizobium symbiovar that nodulate peanut in different regions of China. These findings have practical implications for selecting rhizobial inoculants for peanut cultivation in China.
Article
Multidisciplinary Sciences
Paulo H. da Silva Santos, Joao R. Vieira Manechini, Michael S. Brito, Elisson Romanel, Renato Vicentini, Maximiliano Scarpari, Stephen Jackson, Luciana R. Pinto
Summary: In this study, candidate reference genes for the study of sugarcane flowering were analyzed under different experimental conditions, leading to the identification of UBQ1 and TUB as the most stable reference genes for normalizing gene expression data during floral induction. Furthermore, the research also revealed significant up-regulation of PIL5 and LHP1 in the initial stages of photoperiodic induction of flowering in sugarcane.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Matias Garavaglia, Andres Muzlera, Claudio Valverde
Summary: In the field of prokaryotic taxonomy, there has been a transition towards phylogenomics as the gold standard approach, but it can be costly when managing large amounts of isolates. Multilocus sequence analysis (MLSA) is a recommended alternative due to its affordability and competency. However, the selection criteria for conserved genes for MLSA have not been explicit for different bacterial taxa. This study presents a computational workflow to select internal sequence regions of Pseudomonas core genes for MLSA, which shows comparable phylogenetic resolution to the genome-based ANI approach.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Cell Biology
Celia Maria Quinonez-Flores, Salma Marcela Lopez-Loeza, Cesar Pacheco-Tena, Perla Maria Munoz-Morales, Samara Acosta-Jimenez, Susana Aidee Gonzalez-Chavez
Summary: The study found differences in gene stabilities between CIA and SpAD models in DBA/1 mice, with EF1a, RPL13A, and TBP identified as the best reference genes for different models. These genes enabled data normalization for quantifying inflammatory cytokines, indicating an increase in the expression of IL-1B, IL-12B, IL-17A, and IL-6 in the inflamed joints. Results highlight the importance of validating reference genes before each experiment for obtaining valid and reproducible qPCR data.
INFLAMMATION RESEARCH
(2021)
Article
Biochemical Research Methods
Le Zhang, Zichun Dai, Jun Yu, Ming Xiao
Summary: By reviewing previous studies on CpG-related genes, it is suggested that approximately half of human genes, particularly housekeeping genes, are regulated by CpG islands (CGIs). However, the specific definition of CGIs, their positioning in gene structures, and the regulatory mechanisms associated with CGIs require further explanation. Combining different analysis methods, it has been found that genes associated with high CpG density are more likely to be housekeeping genes, while the characteristics of genes with intermediate CpG density are less distinct.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Adriana Orrego, Maria Cecilia Gavilan, Anibal Arevalos, Belen Ortiz, Belen Gaete Humada, Amiliana Pineda-Fretez, Maria Cristina Romero-Rodriguez, Maria Eugenia Flores Giubi, Man Mohan Kohli, Julio C. M. Iehisa
Summary: This study evaluated the suitability of 12 candidate reference genes for gene expression analysis of M. phaseolina and identified CYP1 as the best reference gene. The findings provide valuable references for gene expression analysis during host infection with M. phaseolina.
Article
Multidisciplinary Sciences
Tania Martin-Perez, Martina Koehsler, Julia Walochnik
Summary: This study evaluated the expression and stability of six commonly used housekeeping genes in N. gruberi and found significant variations in the stability of reference genes depending on the algorithms and experimental conditions. The geNorm, NormFinder, and RefFinder analysis identified ACT and G6PD as the most stable reference genes, while BestKeeper analysis identified 18S and TBP as the most stable reference genes. Additionally, normalizing the expression of the HSP90 gene with the most stable reference genes resulted in reliable gene expression, while using unstable reference genes led to unreliable results. This study has important implications for gene expression studies in N. gruberi.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Nirmal Kumar Sampathkumar, Venkat Krishnan SundaramID, Prakroothi S. Danthi, Rasha Barakat, Shiden Solomon, Mrityunjoy Mondal, Ivo Carre, Tatiana El Jalkh, Aida Padilla-Ferrer, Julien Grenier, Charbel Massaad, Jacqueline C. Mitchell
Summary: The choice of reference genes heavily influences the assessment of differential gene expression by qPCR. Recent studies suggest using RNA-Seq to identify stable genes and statistical approaches to determine the best reference genes. However, this study demonstrates that the statistical approach to determine the best reference genes from commonly used candidates is more important than preselecting stable genes from RNA-Seq data.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Horticulture
Bing He, Hui Chen, Pibiao Shi, Fengqin Hu, Wenjing Song, Lin Meng, Yuanda Lv
Summary: In this study, novel housekeeping and tissue-specific genes were identified in quinoa using different methods, and their expression stability was further evaluated. The results showed that MIF, RGGA, VATE, and UBA2B were the most stable candidate housekeeping genes, while leaf and root-specific genes were also identified. Gene Ontology analysis revealed the functions and enrichment of these genes in quinoa.
Article
Genetics & Heredity
Jianlei Gu, Jiawei Dai, Hui Lu, Hongyu Zhao
Summary: Comprehensive characterization of spatial and temporal gene expression patterns in humans is critical for understanding human diseases. This study proposed a data-driven framework to derive a list of Ubiquitously Expressed Genes (UEGs) and their global expression patterns, providing a valuable resource for further characterizing the human transcriptome.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2023)
Article
Genetics & Heredity
Karim Hasanpur, Sevda Hosseinzadeh, Atiye Mirzaaghayi, Sadegh Alijani
Summary: Accurate normalization of gene expression assays using housekeeping genes is crucial, but there is no consensus on the suitable set of housekeeping genes for quantitative real-time PCR analyses of chicken tissues. This study utilized high-throughput gene expression data to identify the most suitable and stable reference genes for 16 chicken tissues. The results revealed tissue-specific sets of reference genes and disproved the suitability of previously widely used housekeeping genes. The newly identified reference genes can contribute to more accurate normalization for future expression analysis of chicken genes.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Barbara Wrzesinska, Karolina Koscielniak, Patryk Frackowiak, Tadeusz Praczyk, Aleksandra Obrepalska-Steplowska
Summary: The research aimed to identify the most stably expressed reference genes in A. spica-venti plants, crucial for understanding the resistance mechanisms of this plant population to herbicides.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
Esmaeil Basavand, Pejman Khodaygan, Mohammad Moradi, Seyed Abdollah Mousavi, Kristina Lindstrom, Nasser Sedaghati
Summary: This study reported the first occurrence of crown and stem gall caused by Agrobacterium radiobacter on pistachio from Rafsanjan county, Kerman province, Iran, highlighting these bacterial strains as a potential threat to pistachio nurseries in Iran due to their ease of spread through seedlings and agricultural materials.
AUSTRALASIAN PLANT PATHOLOGY
(2022)
Article
Respiratory System
Charlotte Rigauts, Juliana Aizawa, Steven L. Taylor, Geraint B. Rogers, Matthias Govaerts, Paul Cos, Lisa Ostyn, Sarah Sims, Eva Vandeplassche, Mozes Sze, Yves Dondelinger, Lars Vereecke, Heleen Van Acker, Jodie L. Simpson, Lucy Burr, Anne Willems, Michael M. Tunney, Cristina Cigana, Alessandra Bragonzi, Tom Coenye, Aurelie Crabbe
Summary: The presence of Rothia mucilaginosa in the lower airways has an inhibitory effect on pathogen-induced inflammation and is negatively correlated with pro-inflammatory markers in bronchiectasis patients. Mechanistically, R. mucilaginosa inhibits inflammation by reducing NF-kappa B pathway activation. These findings suggest that R. mucilaginosa in the lower airways could potentially mitigate inflammation and impact the severity and progression of chronic respiratory disorders.
EUROPEAN RESPIRATORY JOURNAL
(2022)
Article
Biotechnology & Applied Microbiology
S. A. Mousavi, Y. Gao, P. Penttinen, A. Frostegard, L. Paulin, K. Lindstrom
Summary: A new method based on amplicon sequencing of the rpoB gene has been developed to reliably identify bradyrhizobial strains in nodules and assess their competitiveness compared to other strains.
LETTERS IN APPLIED MICROBIOLOGY
(2022)
Article
Agronomy
Ho Manh Tuong, Sonia Garcia Mendez, Michiel Vandecasteele, Anne Willems, Dexian Luo, Stien Beirinckx, Sofie Goormachtig
Summary: This study isolated the SRS1 strain from salt-resistant Carex distans roots and investigated its effect on the growth of Arabidopsis and tomato. The results showed that SRS1 inoculation promoted plant growth under both saline and nonsaline conditions, including when the plants were grown in white sand and potting soil. Genetic traits related to stress alleviation from both the bacteria and the plants played a crucial role in the impact of this PGPR strain on plant performance.
Article
Plant Sciences
Khawla Oukaltouma, Ahmed El Moukhtari, Yahya Lahrizi, Bouchra Makoudi, Mohammed Mouradi, Mohamed Farissi, Anne Willems, Ahmed Qaddoury, Faouzi Bekkaoui, Cherki Ghoulam
Summary: Water deficit and phosphorus deficiency are severe limitations to agriculture productivity. This study found that phosphorus fertilization can improve the tolerance of faba bean plants to water deficit. Additionally, the combination of water deficit and phosphorus deficiency has a greater impact on plant physiology and biochemistry, with the Reina Mora variety being the most affected.
JOURNAL OF SOIL SCIENCE AND PLANT NUTRITION
(2022)
Article
Microbiology
Judith Van Dingenen, Sonia Garcia Mendez, Stien Beirinckx, Lena Vlaminck, Annick De Keyser, Naomi Stuer, Severine Verschaete, Alexander Clarysse, Joke Pannecoucque, Stephane Rombauts, Isabel Roldan-Ruiz, Anne Willems, Sofie Goormachtig
Summary: Soybeans used for food and feed in Europe have negative impacts due to imports, leading to the need for increased local production and the search for indigenous nodulating strains in Belgium. The study highlights the diverse bacterial richness and the necessity of combining different identification techniques to capture the true nodule rhizobial community. Genomic analysis revealed multiple genetically distinct species capable of nodulating soybeans in laboratory conditions.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Luna M. van der Loos, Sofie D'hondt, Aschwin H. Engelen, Henrik Pavia, Gunilla B. Toth, Anne Willems, Florian Weinberger, Olivier De Clerck, Sophie Steinhagen
Summary: This study investigated the stability and variability of seaweed-associated bacteria across the Atlantic-Baltic Sea salinity gradient. Results showed that bacterial composition was strongly influenced by salinity and host species, with distinct communities in low and high salinity regions. A small taxonomic core community was identified, contributing to 14% of reads per sample, and core taxa followed a gradient model, facilitating host adaptation across the environmental gradient.
Article
Biotechnology & Applied Microbiology
Roba Mohamad, Anne Willems, Antoine Le Quere, Marjorie Pervent, Maurine Bonabaud, Emeric Dubois, Jean-Claude Cleyet-Marel, Brigitte Brunel
Summary: Ten mesorhizobial strains isolated from root-nodules of Anthyllis vulneraria in southern France were classified into two novel species within the genus Mesorhizobium.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2022)
Article
Microbiology
Seyed Abdollah Mousavi, J. Peter W. Young
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Agronomy
Satu Ramula, Seyed Abdollah Mousavi, Aino Kalske
Summary: In this study, the relative effectiveness of different strains of rhizobia on the invasive legume Lupinus polyphyllus was examined. The results showed that the differences in nodulation and plant growth promotion among different strains of the genus Bradyrhizobium were more pronounced in the greenhouse than in the common garden.
Article
Biotechnology & Applied Microbiology
Henry D. Naranjo, Liesbeth Lebbe, Margo Cnockaert, Florent Lassalle, Chin Chin Too, Anne Willems
Summary: Recently, we isolated two closely related strains, LMG 31531T and LMG 31532, from soil and plant roots, respectively. Based on genomic and phenotypic data, these strains differ from previously reported species and are described as a new species, Agrobacterium divergens. Our comparative genomic study also discovered conserved proteins that provide insights into the functional evolution of this genus.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2023)
Article
Pharmacology & Pharmacy
Angelique Rat, Antigoni E. Koletti, Nebojsa Rodic, Vassilios P. Papageorgiou, Anne Willems, Andreana N. Assimopoulou
Summary: In this study, a strain of Pseudomonas sp. R-72008 was found to utilize Alkannin, shikonin, and their derivatives as the sole carbon source. This bacterial strain was able to modify the composition of A/S, decreasing the amount of A/S monomers and increasing the production of A/S oligomers. This research provides new insights into the interactions between bacteria and plant antimicrobials.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Microbiology
Henry D. Naranjo, Angelique Rat, Noemie De Zutter, Emmelie De Ridder, Liesbeth Lebbe, Kris Audenaert, Anne Willems
Summary: Phytopathogenic fungi pose a major threat to global food production, and the use of biocontrol agents derived from medicinal plants could provide an alternative to chemical fungicides. The study identified Pseudomonas sp. strain R-71838 as a promising candidate for biocontrol of fungal pathogens, based on its strong antifungal activity both in vitro and in planta.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Luna M. van der Loos, Lander De Coninck, Roland Zell, Sebastian Lequime, Anne Willems, Olivier De Clerck, Jelle Matthijnssens
Summary: Marine macroalgae (seaweeds) play a vital role in coastal ecosystems as primary producers and foundation species. However, little is known about the diversity and impact of viruses in seaweeds. This study characterized viral communities in healthy and bleached specimens of the commercially important green seaweed Ulva, revealing the presence of diverse and novel viruses. The abundance of certain viruses was significantly higher in the bleached samples, suggesting their possible role in seaweed bleaching.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Josephine A. Adjei, Aregu A. Aserse, Markku Yli-Halla, Benjamin D. K. Ahiabor, Robert C. Abaidoo, Kristina Lindstrom
Summary: The high genetic diversity of Bambara groundnut-nodulating bradyrhizobia in Ghanaian soils was identified through multilocus gene sequence analysis, suggesting a potential vast resource of adapted inoculant strains.
FEMS MICROBIOLOGY ECOLOGY
(2022)
