Review
Biochemistry & Molecular Biology
Atiah H. Almalki
Summary: Lung cancer is the leading cause of cancer-related death worldwide. This review presents recent trends in the analytical techniques used for metabolome mapping of lung cancer, and discusses the potential applications of these techniques in the analysis of biological samples, providing new avenues for treatment strategies and monitoring drug responses.
Article
Biochemistry & Molecular Biology
Simon Lagies, Roman Pichler, Georg Vladimirov, Jana Gawron, Fabian Bazner, Annabell Schreiner, Dajana Kadena, Dietmar A. Plattner, Soeren S. Lienkamp, Bernd Kammerer
Summary: Research has found that the concentration of vancomycin in the kidneys far exceeds plasma levels, potentially leading to nephrotoxic reactions. By studying animal models and cell lines, it was discovered that exposure to vancomycin resulted in metabolic and lipidomic alterations in kidney cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Environmental Sciences
Hongzhi Yao, Xing Li, Yuhao Chen, Guoling Liang, Gao Gao, Huan Wang, Chunlin Wang, Changkao Mu
Summary: The mud crab Scylla paramamosain shows metabolic changes in response to acute salinity reduction, with increased enzyme activities and significant effects on amino acids and energy metabolism pathways. Lipid metabolites play a supporting role in this adaptation process.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Forestry
Yang Liu, Qiu-Yang Chang, Zhong-Hua Tang, Ke-Xin Wu, Ann Abozeid, Li-Qiang Mu
Summary: This study compared the metabolite profiles of Tilia amurensis at different latitudes and found significant differences influenced by environmental factors, especially the annual sunshine percentage. This suggests that T. amurensis exhibits different adaptability to environments at different latitudes.
Article
Biotechnology & Applied Microbiology
Albert Fina, Pierre Millard, Joan Albiol, Pau Ferrer, Stephanie Heux
Summary: By using a high throughput C-13-metabolic flux analysis platform, the metabolic phenotypes of 10 3-HP producing P. pastoris strains were characterized, revealing the impact of NADPH regeneration and cytosolic acetyl-CoA synthesis pathway on metabolic flux distribution. Additionally, the metabolic adaptation of P. pastoris to acidic pH was also investigated.
MICROBIAL CELL FACTORIES
(2023)
Article
Biochemistry & Molecular Biology
Szymon Macioszek, Renata Wawrzyniak, Anna Kranz, Marta Kordalewska, Wiktoria Struck-Lewicka, Danuta Dudzik, Margot Biesemans, Michal Maternik, Aleksandra M. Zurowska, Michal J. Markuszewski
Summary: Renal dysplasia is a severe congenital abnormality of the kidney parenchyma, often leading to end-stage renal failure in childhood and early adulthood. Metabolomics studies have revealed alterations in fatty acid oxidation, amino acid, and purine metabolisms in children with renal dysplasia, offering potential early diagnostic indicators.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Microbiology
Jay Hind Nishad, Arti Singh, Rajnish Bharti, Priyanka Prajapati, Vijay Kumar Sharma, Vijai Kumar Gupta, Ravindra Nath Kharwar
Summary: The study demonstrated that the extract of D. longicolla treated with BRD4770 showed increased antioxidant activity and inhibition zone against S. aureus and MRSA. Analysis revealed induced antibacterial and antioxidant-like compounds in the BRD4770-treated extract, supported by mass spectrometry and high-performance liquid chromatography.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Wentao Xu, Feng Xu, Weijing Song, Le Dong, Jiangchao Qian, Mingzhi Huang
Summary: This study investigated the cellular metabolic mechanism of feeding sodium citrate to enhance SAM production in P. pastoris using metabolomics and metabolic flux analysis. The results showed that sodium citrate had a facilitative effect on SAM production and upregulated the levels of certain metabolites and metabolic pathways involved in methanol metabolism and the TCA cycle. The study proposed that the upregulation of dihydroxyacetone level and the enhancement of citrate synthase activity by acetyl coenzyme A contributed to SAM production. These findings provide new insights into increasing the industrial production of SAM in P. pastoris.
FERMENTATION-BASEL
(2022)
Article
Biochemical Research Methods
Zhentao Liu, Zhengdong Zhang, Sheng Liang, Zhen Chen, Xiaoyao Xie, Tie Shen
Summary: CeCaFLUX is a user-friendly web server that derives metabolic flux distribution from instationary C-13-labeled data through parallel evolutionary optimization. It provides real-time visualization of the flux optimizing process and the ultimate flux outcome. It also functions as a database to enhance the consistency and facilitate sharing of flux studies.
Article
Chemistry, Applied
Ting Zeng, Baohua Fang, Fenglin Huang, Li Dai, Zhi Tang, Jinglin Tian, Guodong Cao, Xuanlin Meng, Yuanchen Liu, Bo Lei, Minghua Lu, Zongwei Cai
Summary: Through metabolomics analysis, it was found that under cadmium stress, most carbohydrates and amino acids were down-regulated as the cadmium concentration increased in rice grains, except for myoinositol which can prevent cadmium toxicity. D-Mannitol and L-cysteine were up-regulated in low-cadmium-accumulating rice with the increase of cadmium concentration. Organic acids, especially 13-(S)-hydroperoxy-9(Z),11(E),15(Z)-octadecatrienoic acid related to alphalinolenic acid metabolism and jasmonic acid production, were activated.
Review
Chemistry, Analytical
Tengfei Yuan
Summary: Analyzing steroids in different biological matrices helps gain insight into the status of steroids.
MICROCHEMICAL JOURNAL
(2022)
Article
Agronomy
Archis Pandya, Bjorn Thiele, Andres Zurita-Silva, Bjorn Usadel, Fabio Fiorani
Summary: The study evaluated saponin content and their corresponding sapogenins in 114 different quinoa accessions, showing considerable variability in saponin content in quinoa. Approximately 75% of the genotypes were classified as low-saponin content lines, which is promising for current and future quinoa breeding programs. Additionally, twelve saponins of the oleanane type were identified, including a previously unreported compound, contributing to the valorization of genetic resources for quinoa.
Review
Medical Laboratory Technology
Stephanie Rankin-Turner, Liam M. Heaney
Summary: Mass spectrometry (MS) has become a powerful and versatile tool in clinical laboratory, with advancements in biomarker detection, protein measurement, therapeutic drug monitoring, and automation leading to potential revolution in clinical testing.
CLINICAL CHEMISTRY AND LABORATORY MEDICINE
(2023)
Article
Environmental Sciences
C. D. Metcalfe, S. Bayen, M. Desrosiers, G. Munoz, S. Sauve, V Yargeau
Summary: Endocrine disrupting chemicals (EDCs) are a diverse group of chemicals that require sensitive and varied analytical methods to monitor their presence in the environment. Only environmental matrixes with a clear link to endocrine effects are included, and emerging methods and advanced instruments for sample preparation are also discussed.
ENVIRONMENTAL RESEARCH
(2022)
Article
Horticulture
Jung-Sung Chung, Hyeong-Cheol Kim, Su-Min Yun, Hyun-Jin Kim, Cheol-Soo Kim, Jeung-Joo Lee
Summary: Sulfur is an essential nutrient for plant growth and metabolism, and significantly affects the growth and metabolites of lettuce. Higher sulfur concentration treatment resulted in increased growth and metabolite content in lettuce compared to lower sulfur concentration treatment.
Article
Biochemical Research Methods
Juan J. Barrero, Alejandro Pagazartaundua, Benjamin S. Glick, Francisco Valero, Pau Ferrer
Summary: Pichia pastoris has been identified as having a bottleneck at the ER translocation level, with an improved secretion signal leading to increased production of target proteins and supporting higher maximum specific growth rates.
Article
Biochemistry & Molecular Biology
David Lao-Martil, Koen J. A. Verhagen, Joep P. J. Schmitz, Bas Teusink, S. Aljoscha Wahl, Natal A. W. van Riel
Summary: This review evaluates the metabolic models for Saccharomyces cerevisiae and finds that there is no commonly applicable model at present. Although significant progress has been made in understanding the kinetic glycolytic mechanisms, there are still uncertainties in the model topology and parameter values. Improvements in experimental measurement technologies and computational tools create opportunities to extend the model scale and consider external regulation. Furthermore, the availability of new individual cell data will enable the models to characterize the heterogeneity of the population and provide unseen possibilities for industrial fermentation improvement.
Article
Multidisciplinary Sciences
Karel Olavarria, Yared O. Pijman, Ricardo Cabrera, Mark C. M. van Loosdrecht, S. Aljoscha Wahl
Summary: The cofactor preference of the acetoacetyl-CoA reductase encoded by the phaB1 gene from Cupriavidus necator was studied in relation to PHB accumulation.
SCIENTIFIC REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Martina Pasini, Alfred Fernandez-Castane, Gloria Caminal, Tim W. Overton, Pau Ferrer
Summary: This study investigates the suitability of a set of IPTG-inducible protein expression systems in bioprocess conditions resembling industrial settings, and successfully improves the production yield and advantageous features of recombinant proteins through several generations of engineering.
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Albert Fina, Stephanie Heux, Joan Albiol, Pau Ferrer
Summary: This study improves the productivity of Pichia pastoris in producing 3-hydroxypropionic acid by combining different metabolic engineering approaches. The results show that, in combination with using glycerol as a carbon source, the metabolically engineered strains achieved the highest concentration and productivity of 3-hydroxypropionic acid reported so far in yeast.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Correction
Biotechnology & Applied Microbiology
Albert Fina, Stephanie Heux, Joan Albiol, Pau Ferrer
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Engineering, Environmental
Timothy Paez-Watson, Mark C. M. van Loosdrecht, S. Aljoscha Wahl
Summary: Understanding microbial communities and their regulation is important for new technologies. Resource allocation and biosynthesis in microbial communities are poorly understood. In this study, metabolic flux analysis was used to study the optimal phenotype of polyphosphate accumulating organisms (PAOs). The results validate limited anaerobic biosynthesis in PAOs and identify temperature-dependent resource allocation strategies.
Article
Multidisciplinary Sciences
Carla Ines Soares Rodrigues, Maxime den Ridder, Martin Pabst, Andreas K. Gombert, Sebastian Aljoscha Wahl
Summary: The identity and amount of carbon sources have significant impacts on the growth and physiology of microbial species. This study compared the proteomes of Saccharomyces cerevisiae cells grown on sucrose or glucose as the sole carbon source. Different strains exhibited different physiological responses to sucrose, with some showing higher growth rates on sucrose while others showed the opposite.
SCIENTIFIC REPORTS
(2023)
Article
Biotechnology & Applied Microbiology
Alvaro Calvillo, Teresa Pellicer, Marc Carnicer, Antoni Planas
Summary: In this study, the production of vitamin B-12 using the Propionibacterium freudenreichii NBRC 12391 wild-type strain was characterized and optimized in shake flasks. It was found that the addition of 5,6-dimethylbenzimidazole (DMBI) and the induction time had significant effects on vitamin B-12 production. Batch and fed-batch bioprocesses were not suitable for high volumetric productivities, thus an anaerobic single-phase continuous bioprocess strategy was developed.
MICROBIAL CELL FACTORIES
(2023)
Article
Biotechnology & Applied Microbiology
Albert Fina, Pierre Millard, Joan Albiol, Pau Ferrer, Stephanie Heux
Summary: By using a high throughput C-13-metabolic flux analysis platform, the metabolic phenotypes of 10 3-HP producing P. pastoris strains were characterized, revealing the impact of NADPH regeneration and cytosolic acetyl-CoA synthesis pathway on metabolic flux distribution. Additionally, the metabolic adaptation of P. pastoris to acidic pH was also investigated.
MICROBIAL CELL FACTORIES
(2023)
Article
Biotechnology & Applied Microbiology
Gabriela C. Breda, Priscila E. Faria, Yuri S. Rodrigues, Priscila B. Pinheiro, Maria Clara R. Nucci, Pau Ferrer, Denise M. G. Freire, Rodrigo V. Almeida, Rafael D. Mesquita
Summary: ProspectBIO is a new software for bioprospecting that can efficiently find non-annotated enzyme sequences by searching for homologs in genomes. Using this software, a novel lipase-encoding gene from Ustilago hordei was discovered and successfully expressed in yeast, resulting in an active enzyme.
Article
Biotechnology & Applied Microbiology
Karel Olavarria, Marco V. Becker, Diana Z. Sousa, Mark C. M. van Loosdrecht, S. Aljoscha Wahl
Summary: This study proposes a novel metabolic engineering strategy to achieve efficient anaerobic production of poly-(R)-3-hydroxybutyrate (PHB) in Escherichia coli. The strategy involves rerouting the glycolytic flux through non-oxidative glycolysis and coupling PHB synthesis with NADH re-oxidation. Stoichiometric analysis and various thermodynamic approaches were used to assess the feasibility and bottlenecks of the engineered pathway.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2023)
Review
Biotechnology & Applied Microbiology
Alvaro Calvillo, Teresa Pellicer, Marc Carnicer, Antoni Planas
Summary: This review provides an overview of the historical research and biosynthetic characteristics of vitamin B-12, as well as the current state, advances, and challenges of its industrial production. The potential applications of vitamin B-12 in different markets are also discussed.
BIOENGINEERING-BASEL
(2022)