Article
Environmental Sciences
Manuja U. Lekammudiyanse, Megan I. Saunders, Nicole Flint, Andrew Irving, Emma L. Jackson
Summary: Zostera muelleri, an abundant seagrass species in subtropical coastal areas of Australia, is influenced by tidal height and light intensity for flowering. A laboratory experiment showed that the subtidal-unshaded conditions resulted in the earliest and highest flowering intensity, while no flowering occurred in the intertidal-shaded conditions. Therefore, subtidal-unshaded conditions should be applied in seagrass nurseries to enhance flower abundance.
MARINE ENVIRONMENTAL RESEARCH
(2023)
Article
Plant Sciences
A. Skiljaica, M. Jagic, T. Vuk, D. Leljak Levanic, N. Bauer, L. Markulin
Summary: Increases in environmental temperature have significant effects on plant growth and development, and this study identified reliable reference genes for Arabidopsis thaliana experiments involving elevated temperature treatments. The identification of these reference genes contributes to a better understanding of the impact of climate change on plants, particularly in agricultural species.
Article
Environmental Sciences
Manuja U. Lekammudiyanse, Megan I. Saunders, Nicole Flint, Andrew Irving, Emma L. Jackson
Summary: Flowering plays a crucial role in the genetic diversity and resilience of seagrass meadows. This study investigates the effects of tidal exposure on flowering variabilities in patchy intertidal meadows and finds that plant cover and exposure duration significantly influence flowering density and frequency.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Alice Nevone, Francesca Lattarulo, Monica Russo, Giada Panno, Paolo Milani, Marco Basset, Maria Antonietta Avanzini, Giampaolo Merlini, Giovanni Palladini, Mario Nuvolone
Summary: In the next-generation sequencing era, RT-qPCR remains widely used for quantifying nucleic acids due to its popularity, versatility, and cost-effectiveness. However, accurate measurement of transcriptional levels requires appropriate reference genes for normalization. Here, we present a strategy that utilizes publicly available transcriptomic datasets to select suitable reference genes for specific clinical or experimental settings and includes a pipeline for RT-qPCR assay design and validation. We demonstrated the efficacy of this strategy by identifying and validating reference genes for transcriptional studies of bone-marrow plasma cells in AL amyloidosis patients. This strategy can be applied to other settings with publicly available transcriptomic datasets.
Article
Biochemistry & Molecular Biology
Olga V. V. Nadei, Natalia I. I. Agalakova
Summary: Normalization of RT-qPCR data using stable reference genes is critical for reliable results. This study analyzed the expression of reference genes in cortex and hippocampus of rats exposed to excessive fluoride, and identified the most valid genes for mRNA quantification.
BIOLOGICAL TRACE ELEMENT RESEARCH
(2023)
Article
Environmental Sciences
Ju Mu, Yu Wang, Miao Wang, Dayi Zhang, Mingying Liu
Summary: This study constructed a mouse model exposed to poly-propylene microplastics (PP-MPs) to evaluate the bioaccumulation of PP-MPs in the kidney and explore potential reference genes using RT-qPCR. The stability and reliability of 19 candidate reference genes were assessed using four algorithms, and the top five most stable genes were determined (Cox4i1, Rps3, Rps9, Rps18, and Gapdh). Three genes associated with different biochemical processes were chosen to verify the identified reference genes, showing different expression profiles and emphasizing the importance of selecting reliable reference genes.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Plant Sciences
Maria Noelia Ulrich, Esteban Muniz-Padilla, Alejandra Corach, Esteban Hopp, Daniela Tosto
Summary: This study evaluated the stability of different reference genes of glyphosate-resistant S. halepense, finding that PP2A and ARI8 were the most stable genes. The results provide valuable information for gene expression analysis under glyphosate stress and will facilitate resistance mechanism studies in this weed species.
Article
Fisheries
Shuaijie Sun, Zhitong Wang, Dongdong Yuan, Mengke Ni, Huifen Xu, Wanliang Wang, Chi Zhang, Meiqun Chen, Lamu ZhaXi, Jianshe Zhou, Ming Li
Summary: This study used RT-qPCR technology to investigate the expression of eight candidate genes in different tissues, developmental stages, and under bacterial stress in Salmo trutta. The stability of these genes was ranked using comprehensive analysis software. The results showed that the expression of the hprt1 gene was relatively stable under different conditions.
AQUACULTURE REPORTS
(2022)
Article
Forestry
Zhaoli Chen, Xiaogang Bai, Xiangyang Li, Bingshan Zeng, Bing Hu
Summary: The study evaluated the expression stability of ten candidate genes in Acacia melanoxylon using five different algorithms. The results showed that certain genes maintained stable expression under different conditions, which provides a reference for further gene expression analysis in this species.
Article
Biochemistry & Molecular Biology
Chaofan Jiang, Lin Zhou, Qingchen Zhao, Mengke Wang, Sirui Shen, Te Zhao, Kaidi Cui, Leiming He
Summary: This study validated the expression stability of seven candidate reference genes in Sclerotium rolfsii under different conditions and recommended suitable reference gene combinations for RT-qPCR normalization. The results showed that using one or two reference genes to normalize the expression of target genes in S. rolfsii did not significantly differ.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Jiao Chen, Yunjian Wang, Zhi Yang, Danwen Liu, Yao Jin, Xixi Li, Yuhang Deng, Boya Wang, Zhifeng Zhang, Yubin Ma
Summary: This study identified suitable reference genes in U. unicinctus based on transcriptome data and discovered some new stable reference genes. The findings provide important information for future gene expression studies in U. unicinctus.
Article
Agriculture, Dairy & Animal Science
Juan Zhao, Cheng Wang, Lin Zhang, Aiai Lei, Linjie Wang, Lili Niu, Siyuan Zhan, Jiazhong Guo, Jiaxue Cao, Li Li, Hongping Zhang, Tao Zhong
Summary: The rumen is essential for the absorption of energy substrate in ruminants, and understanding the gene expression profiles is crucial for exploring the regulatory mechanisms of rumen development in goats. This study identified 16 candidate reference genes from transcriptome sequencing of goat rumen tissues, and demonstrated that RPS4X and RPS6 were the most stable reference genes for quantifying gene expression in rumen tissues via RT-qPCR analysis.
Article
Horticulture
Yuanlei Chen, Yuting Yuan, Zihui Qiu, Weijin Hong, Ke Mao, Chunchao Yao, Zhande Liu, Nannan Wang
Summary: Selecting appropriate reference genes is crucial for the accuracy of gene expression analysis. However, reference genes have not been identified in kiwifruit roots and across kiwifruit species, and the reference genes for iron deficiency have not been validated. In this study, ten candidate reference genes were assessed for their suitability in different kiwifruit tissues under iron deficiency conditions. The recommended reference genes were validated using six target genes involved in iron uptake and transport. These results provide a basis for improving the accuracy of gene expression analysis and understanding the molecular mechanisms of iron deficiency adaptation in kiwifruit species.
SCIENTIA HORTICULTURAE
(2023)
Article
Plant Sciences
Judit Tajti, Magda Pal, Tibor Janda
Summary: Oat, a widely cultivated cereal with high nutritional value, shows different stability of reference gene expression under diverse abiotic stress conditions. ADPR was identified as the top-rated reference gene for all samples, while TUB and EF1 were most affected by the treatments.
Article
Plant Sciences
Leandro Francisco de Oliveira, Amanda Rusiska Piovezani, Dimitre A. Ivanov, Leonardo Yoshida, Eny Iochevet Segal Floh, Massuo Jorge Kato
Summary: This study identified stable reference genes for gene expression analysis in four Piper species and provided a list of recommended gene pairs for each species. These findings will facilitate further transcriptomic and functional gene research.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2022)
Review
Engineering, Biomedical
Javiera Sanhueza Ortega, Rocio Corrales-Orovio, Peter Ralph, Jose Tomas Egana, Carmine Gentile
Summary: 3D bioprinting technology has the potential to revolutionize the biomedical field by enabling tissue engineering and regeneration. However, there are challenges to be addressed, such as the lack of tissue oxygenation in bioprinted tissues and organs. Recent approaches, including the use of photosynthetic microorganisms, offer promising solutions to improve tissue oxygenation. This review summarizes the state-of-the-art approaches and discusses the application of photosynthetic microorganisms in 3D bioprinting.
ACTA BIOMATERIALIA
(2023)
Review
Environmental Sciences
Luong N. Nguyen, Minh T. Vu, Hang P. Vu, Md. Abu Hasan Johir, Leen Labeeuw, Peter J. Ralph, T. M. I. Mahlia, Ashok Pandey, Ranjna Sirohi, Long D. Nghiem
Summary: This paper reviews the current state of microalgal culture development for carbon capture and utilization (CCU) and highlights its potential contribution to addressing climate change challenges. Innovative system designs are crucial to achieve large-scale CO2 capture by microalgae, and downstream processes of microalgal culture are important for the overall success of microalgae-based CCU.
CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Shawn Price, Unnikrishnan Kuzhiumparambil, Mathieu Pernice, Andrei Herdean, Peter Ralph
Summary: Poly-hydroxy-butyrate (PHB) bioplastic resin can be produced from atmospheric CO2 using cyanobacteria. Random mutagenesis combined with FACS was used to select mutants with higher lipid content, resulting in two strains with significantly increased PHB yields, biomass accumulation, and volumetric PHB density. The highest PHB yielding strain was 43% higher than the wild type, and the highest volumetric PHB density was 75% higher. This study shows the potential of random chemical mutagenesis and FACS in increasing PHB productivity in cyanobacteria, making bioplastic production economically viable.
BIOPROCESS AND BIOSYSTEMS ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Harvey Bates, Alonso Zavafer, Milan Szabo, Peter J. Ralph
Summary: This work presents a method to estimate ETRII in real-time through predictive statistical modeling, utilizing the Kautsky induction curve and a low-cost chlorophyll a fluorometer. The method allows for a high-throughput and high-resolution assessment of ETRII, providing a faster alternative to quenching analysis with lower production costs and technical requirements.
JOURNAL OF APPLIED PHYCOLOGY
(2023)
Article
Plant Sciences
Andrei Herdean, Christopher Hall, David J. Hughes, Unnikrishnan Kuzhiumparambil, Bernardo Campos Diocaretz, Peter J. Ralph
Summary: Light intensity and temperature have independent impacts on the photosynthetic machinery. In this study, we found that PAM measurements at different temperatures produce significantly different results in the chlorophyte Chlorella vulgaris. We also discovered that temperature plays a crucial role in non-photochemical quenching, and previous temperature acclimation does not affect it.
PHOTOSYNTHESIS RESEARCH
(2023)
Article
Geosciences, Multidisciplinary
Martino E. Malerba, Micheli Duarte de Paula Costa, Daniel A. Friess, Lukas Schuster, Mary A. Young, David Lagomasino, Oscar Serrano, Sharyn M. Hickey, Paul H. York, Michael Rasheed, Jonathan S. Lefcheck, Ben Radford, Trisha B. Atwood, Daniel Ierodiaconou, Peter Macreadie
Summary: Blue carbon ecosystems (BCE), such as mangrove forests, tidal marshes, and seagrass meadows, are threatened and their contribution to mitigating climate change is at risk. Remote sensing provides a promising and cost-effective method for accounting BCE at large scales. This review provides guidelines for using remote sensing technologies to develop cost-effective carbon inventories for BCE and supports the UNFCCC in incorporating blue carbon into climate change policies.
EARTH-SCIENCE REVIEWS
(2023)
Article
Biochemistry & Molecular Biology
Hung Manh Nguyen, Miriam Ruocco, Emanuela Dattolo, Federica Paola Cassetti, Sebastiano Calvo, Agostino Tomasello, Lazaro Marin-Guirao, Mathieu Pernice, Gabriele Procaccini
Summary: This study examined the adaptation of Posidonia oceanica to local environmental conditions, focusing on the Stagnone di Marsala coastal lagoon. Results showed higher salinity and temperature levels within the lagoon compared to the outer lagoon regions. Genetic analysis revealed genetic isolation and high clonality of the innermost site, with certain outlier loci associated with plant stress response and development regulation. This study provides important insights into the genetic basis of seagrass adaptation to local conditions.
Article
Environmental Sciences
Micheli Duarte de Paula Costa, Maria Fernanda Adame, Catherine V. Bryant, Jack Hill, Jeffrey J. Kelleway, Catherine E. Lovelock, Anne Ola, Michael A. Rasheed, Cristian Salinas, Oscar Serrano, Nathan Waltham, Paul H. York, Mary Young, Peter Macreadie
Summary: Vegetated coastal ecosystems, particularly mangroves, tidal marshes, and seagrasses, are effective in sequestering and storing carbon, making them valuable for climate change mitigation and adaptation. A study in Queensland, Australia estimated that the total sedimentary organic carbon stocks in the state were 569 +/- 98 Tg C, with the majority occurring in three regions. Protected areas in Queensland play a significant role in conserving these carbon assets in coastal wetlands.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Multidisciplinary Sciences
Alex B. Carter, Rob Coles, Jessie C. Jarvis, Catherine V. Bryant, Timothy M. Smith, Michael A. Rasheed
Summary: Report cards that monitor environmental trends are effective communication tools, as they are easily understood and accessible to the general public, scientists, managers, and policy makers. In this study, a report card method for seagrass was developed using long-term monitoring data, incorporating spatial and temporal variability in three metrics. This framework provides reliable comparisons of seagrass condition and was applied to an industrial port in the Great Barrier Reef World Heritage Area in northeastern Australia.
SCIENTIFIC REPORTS
(2023)
Editorial Material
Biochemistry & Molecular Biology
Peter J. Ralph, Mathieu Pernice
Summary: Photosynthesis can be utilized to capture carbon and promote greener industries. The use of algae-driven carbon capture and manufacturing technology has the potential to reduce CO2 emissions while also generating commodities like bioplastics.
Article
Biotechnology & Applied Microbiology
Kate Scardifield, Nahum Mclean, Unnikrishnan Kuzhiumparambil, Peter J. Ralph, Nicolas Neveux, Geoff Isaac, Tim Schork
Summary: This paper presents the potential of using seaweed in construction to reduce embodied carbon. Through exploring the historical and current uses of seaweed in the industry, the study identifies opportunities for the development of seaweed-based construction materials. It emphasizes the importance of interdisciplinary research collaborations and showcases a case study on the design and production of seaweed bricks, highlighting their potential for carbon storage in the built environment.
JOURNAL OF APPLIED PHYCOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Breanna Osborne, Nachshon Siboni, Justin R. Seymour, Peter Ralph, Mathieu Pernice
Summary: This study explores the potential of combining mutualistic species as a consortium to enhance antibacterial properties against Vibrio parahaemolyticus. The combination of Tetraselmis sp. and Pseudoalteromonas peptidolytica shows the greatest inhibition rate of V. parahaemolyticus. This probiotic consortia has the potential for use as a biocontrol technique within mariculture.
JOURNAL OF APPLIED PHYCOLOGY
(2023)
Article
Plant Sciences
Tajamul Hussain, David J. Mulla, Nurda Hussain, Ruijun Qin, Muhammad Tahir, Ke Liu, Matthew T. Harrison, Sutinee Sinutok, Saowapa Duangpan
Summary: This study evaluated the ability of CSM-CERES-Rice model to determine the optimal N fertilization rate for different sowing dates of upland rice. The model performed well in calibration and validation, and could be used to determine the economically optimal N fertilization rate for different sowing windows, maximizing the productivity and profitability of upland rice production.
Review
Biotechnology & Applied Microbiology
Sara Hamzelou, Damien Belobrajdic, James A. Broadbent, Angela Juhasz, Kim Lee Chang, Ian Jameson, Peter Ralph, Michelle L. Colgrave
Summary: Protein derived from algae has great potential to provide high-quality protein foods for the growing human population. Proteomic investigations can provide insights into the composition and biochemistry of microalgae, aiding in the identification and cultivation of algae strains that produce high-quality protein. Current research has focused on pathways related to lipid production.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2023)