Article
Biochemistry & Molecular Biology
Eugene Korotkov, Yulia Suvorova, Dimitry Kostenko, Maria Korotkova
Summary: We have developed a de novo method called the IP method for identifying dispersed repeats with low substitution rates. The IP method outperforms previously developed methods in detecting dispersed repeats with an average substitution rate of 1.5 or less. Using the IP method, we found three families of dispersed repeats in the genomes of E. coli and other bacterial species, constituting a significant portion of their genomes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Vincent Okelo Wanga, Xiang Dong, Millicent Akinyi Oulo, Elijah Mbandi Mkala, Jia-Xin Yang, Guy Eric Onjalalaina, Moses Kirega Gichua, Paul Muigai Kirika, Robert Wahiti Gituru, Guang-Wan Hu, Qing-Feng Wang
Summary: The study investigated the complete chloroplast genome of the Chinese endemic Acanthochlamys bracteata and compared it with African Xerophyta species, revealing genetic relationships and genomic characteristics. Variations were found in gene number, repeat sequences, and nucleotide diversity among the species, providing insights for genetic variability and evolutionary studies in Velloziaceae.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Multidisciplinary Sciences
Yirong Shi, Yiwei Niu, Peng Zhang, Huaxia Luo, Shuai Liu, Sijia Zhang, Jiajia Wang, Yanyan Li, Xinyue Liu, Tingrui Song, Tao Xu, Shunmin He
Summary: This study presents a comprehensive map of 366,013 polymorphic short tandem repeats (pSTRs) in the human genome, based on deeply sequenced genomes. The study explores the associations between STR mutations and various genomic features, such as gene expression and alternative polyadenylation. It also investigates population differentiation and genotypes disease-causing STRs.
NATURE COMMUNICATIONS
(2023)
Article
Neurosciences
Shu Guo, Lien Nguyen, Laura P. W. Ranum
Summary: Microsatellite-expansion mutations can produce toxic expansion RNAs and various types of RAN proteins, leading to neuropathological changes and dysregulation of key pathways. The mechanism of RAN protein production without canonical or close-cognate AUG initiation codons is not fully understood, but RNA structure, flanking sequences, and stress pathways have been shown to be important factors.
CURRENT OPINION IN NEUROBIOLOGY
(2022)
Article
Forestry
Shufen Chen, Wataru Ishizuka, Yamato Unno, Kazutaka Kusunoki, Susumu Goto
Summary: Pollen dispersal patterns and male reproductive success play crucial roles in seed orchard management. Pedigree reconstruction and paternity analysis are important for selecting potential superior paternal clones. This study examined the pollen dispersal pattern in an open-pollinated seed orchard and evaluated the performance of different paternal clones.
TREE GENETICS & GENOMES
(2022)
Article
Genetics & Heredity
Satomi Mitsuhashi, Martin C. Frith, Naomichi Matsumoto
Summary: The study conducted a genome-wide survey of human tandem repeats using long read genome sequencing data, finding that known disease-associated tandem repeats are generally longer and more polymorphic in the population. Additionally, the lengths of disease-causing tandem repeats were found to be correlated with nearby GWAS SNP genotypes.
BMC MEDICAL GENOMICS
(2021)
Article
Multidisciplinary Sciences
Chrystian Aparecido Grillo Haerter, Daniel Rodrigues Blanco, Josiane Baccarin Traldi, Eliana Feldberg, Vladimir Pavan Margarido, Roberto Laridondo Lui
Summary: The distribution pattern of microsatellites is a challenging problem in fish cytogenetics. Most species have similar patterns of the (GATA)(n) microsatellite in the histone genes and 5S rDNA carriers. However, there are chromosomal polymorphisms in specific species.
Article
Plant Sciences
Qian Zhou, Yun Chen, Jilian Wang, Mingyuan Li, Weijun Zeng, Yuzhou Wang, Yanhong Li, Huixin Zhao
Summary: This study analyzed the chloroplast genome sequences of five medicinal plants from the genus Lepidium, revealing genetic profiles and differences among them. The analysis showed differences in repeat sequences and codon usage, indicating the influence of mutation and natural selection. The findings have implications for breeding, species recognition, phylogenetic evolution, and chloroplast genetic engineering of Lepidium medicinal plants.
FUNCTIONAL PLANT BIOLOGY
(2023)
Article
Mathematical & Computational Biology
Kenny da Costa Pinheiro, Bruna Veronica Azevedo Gois, Wylerson Guimaraes Nogueira, Fabricio Almeida Araujo, Ana Lidia Cavalcante Queiroz, Oscar Cardenas-Alegria, Artur Luiz da Costa da Silva, Antonio Marcio Gomes Martins Junior, Rommel Thiago Juca Ramos
Summary: This study reveals the existence of microsatellite polymorphisms in the genome of Corynebacterium pseudotuberculosis, which can be used for strain identification. In addition, the SSR locations responsible for bacterial adherence were identified by evaluating the SSR similarities among different serum variants. Statistical analysis shows that the microsatellite groups belonging to equi and ovis biovars have a significant similarity, indicating them as potential biomarkers for C. pseudotuberculosis.
FRONTIERS IN BIOINFORMATICS
(2022)
Article
Philosophy
Donald Mark C. Ude
Summary: The sense of interconnectedness in African thought is best described in epistemic terms, as it is primarily a mode of knowing/perceiving the world. The epistemic idiom is useful for formulating emancipatory demands and building epistemic alliances against the subjugation of African and non-Western knowledges by colonial mechanisms.
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)
Editorial Material
Biochemistry & Molecular Biology
Vesselin Baev, Andreas Gisel, Ivan Minkov
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(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.
Correction
Forestry
Valeriu-Norocel Nicolescu, William L. Mason, Jean-Charles Bastien, Torsten Vor, Krasimira Petkova, Vilem Podrazsky, Martina Dodan, Sanja Peric, Nicola La Porta, Robert Brus, Sinisa Andrasev, Martin Slavik, Juraj Modransky, Michal Pastor, Karoly Redei, Branislav Cvjetkovic, Ahmet Sivacioglu, Vasyl Lavnyy, Cornelia Buzatu-Goanta, Gheorghe Mihailescu
JOURNAL OF FORESTRY RESEARCH
(2023)
Article
Oncology
Vesselin Baev, Danijela Koppers-Lalic, Bruno Costa-Silva
Article
Green & Sustainable Science & Technology
Marina Zanardo, Matteo Giannattasio, Gaurav Sablok, Massimo Pindo, Nicola La Porta, Michele Lorenzetti, Carlo Noro, Piergiorgio Stevanato, Giuseppe Concheri, Andrea Squartini
Summary: Horn manure is a biodynamic agricultural product made from cow fecal material fermented in cow horns. In this study, the changes in bacterial and fungal communities during the maturation of horn manure were analyzed. The microbial community showed a significant shift from Firmicutes to Proteobacteria and later to Actinobacteria. The most abundant fungus in the starting fecal material belonged to the Onygenales order, suggesting a link between manure and horn degradation processes.
ENVIRONMENT DEVELOPMENT AND SUSTAINABILITY
(2023)
Article
Microbiology
Vesselin Baev, Elena Apostolova, Velitchka Gotcheva, Miglena Koprinarova, Maria Papageorgiou, Joao Miguel Rocha, Galina Yahubyan, Angel Angelov
Summary: Sourdoughs are microbial ecosystems composed of lactic acid bacteria and acid-tolerant yeasts, which significantly impact the characteristics of bakery products. By studying the microbial communities in Bulgarian sourdoughs, we found that the composition of the microbiome varies significantly depending on geographical location, potentially due to climate and geographic factors.
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
Microbiology
Daniela Mollova, Mariyana Gozmanova, Elena Apostolova, Galina Yahubyan, Ilia Iliev, Vesselin Baev
Summary: Lactiplantibacillus plantarum is a diverse species of lactic acid bacteria found in various ecological niches. This study focused on the L. plantarum PU3 strain, which has potential as a probiotic agent. Genomic analysis revealed the strain's genetic determinants for various beneficial traits, while phenotypic analysis confirmed its tolerance to challenging environments. The absence of virulence factors and the presence of potential antimicrobial activity further highlight its promising potential for probiotic and therapeutic applications.
Article
Biotechnology & Applied Microbiology
Ivelina Vassileva, Vesselin Baev, Galina Yahubyan, Elena Apostolova-Kuzova, Angel Angelov, Miglena Koprinarova
Summary: This study used next-generation sequencing to analyze the microbial ecosystem of a whole grain sourdough from Southwest Bulgaria. The results showed the presence of lactic acid bacteria and yeast in the sourdough. A standardized DNA extraction protocol was developed, which allows accurate assessment of the microbiota of sourdough samples.
FOOD TECHNOLOGY AND BIOTECHNOLOGY
(2023)
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)
