Article
Plant Sciences
Pengpeng Li, Zuying Liao, Jingzhe Zhou, Liyan Yin, Hong Sheng Jiang, Wei Li
Summary: Submerged macrophytes have developed the ability to use bicarbonate to mitigate the effects of photorespiration, leading to increased oxygen production. Experiments have shown that inhibiting bicarbonate use with a carbonic anhydrase inhibitor significantly reduces oxygen production rate in three out of four studied submerged macrophytes, while the species that solely use CO2 are not affected.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Article
Chemistry, Multidisciplinary
Marta Meneghello, Ana Rita Oliveira, Aurore Jacq-Bailly, Ines A. C. Pereira, Christophe Leger, Vincent Fourmond
Summary: Mo/W formate dehydrogenases catalyze the reversible reduction of CO2 to formate, and it has been definitively demonstrated through an electrochemical method that the substrate is indeed CO2, not a hydrated species like HCO3-.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biotechnology & Applied Microbiology
Zhizhuo Shao, Xiujun Xie, Xueying Liu, Zhenbing Zheng, Li Huan, Baoyu Zhang, Guangce Wang
Summary: There is no clear evidence of an operative xanthophyll cycle in species containing phycobilisomes, including red algae and cyanobacteria. However, research has found that the gamma-type carbonic anhydrase-like1 (gamma CAL1) protein in mitochondria plays a key photoprotective role in the red algae Neopyropia yezoensis, by transforming CO2 produced by photorespiration into bicarbonate to prevent CO2 escape and increase the partial pressure of CO2 near Rubisco. This mechanism promotes the efficiency of the Calvin cycle and helps red algae resist high light stress.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2022)
Article
Engineering, Chemical
Yu-Chieh Lin, Chengfeng Xue, Shih- Tan, Wan-Wen Ting, Shih-Chen Yang, I-Son Ng
Summary: A new assay based on pH value decline was established to quantify the activity of decarboxylase and capture released CO2. RuBisCo was hardly co-expressed with CadA in cascade enzymatic reaction. The strain with CadA and CA released the least amount of CO2 and had the best CO2 assimilation capability.
JOURNAL OF THE TAIWAN INSTITUTE OF CHEMICAL ENGINEERS
(2022)
Review
Biochemistry & Molecular Biology
Ashok Aspatwar, Leo Syrjanen, Seppo Parkkila
Summary: Zebrafish have become a crucial model organism for studying various physiological and biological phenomena. Carbonic anhydrases (CAs) and carbonic anhydrase related proteins (CARPs) play important roles in multiple physiological processes, including pigmentation and motor coordination in zebrafish. Disruption of these proteins' function in zebrafish can have lethal outcomes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biophysics
Iryna Antal, Martina Koneracka, Martina Kubovcikova, Vlasta Zavisova, Alena Jurikova, Iryna Khmara, Maria Omastova, Matej Micusik, Monika Barathova, Lenka Jelenska, Ivana Kajanova, Miriam Zatovicova, Silvia Pastorekova
Summary: Antibody-modified magnetic nanoparticles were successfully prepared and demonstrated the ability to target cancer cells specifically by conjugating specific monoclonal antibodies on their surface. The internalization of these nanoparticles into tumor cells expressing hypoxic marker was confirmed, showing their potential for targeted cancer therapy.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2021)
Review
Agronomy
Yanyou Wu, Yansheng Wu
Summary: Plant photosynthesis and rock chemical dissolution are two of the most important CO2 sequestration processes on Earth. The coupling of karstification and photosynthesis can increase the capacity of carbon sinks. Developing karst-adaptable plants can strengthen the coupling and improve the carbon sink capacity of karst ecosystems.
Article
Chemistry, Analytical
Dounia Elfadil, Sara Palmieri, Flavio Della Pelle, Manuel Sergi, Aziz Amine, Dario Compagnone
Summary: This study presents a novel method combining molecularly imprinted polymers (MIPs) and enzymatic inhibition assay for the selective and sensitive determination of acetazolamide (ACZ) in biological samples. The MIPs were synthesized using ACZ as the template molecule and were used as the sorbent phase in dispersive solid-phase extraction (MIPs-dSPE). The developed method showed good recovery and correlation with LC-MS/MS analysis, providing a selective and quantitative approach for the determination of ACZ.
Article
Oncology
Marwa E. Elsherbiny, Mohammed Shaaban, Rana El-Tohamy, Islam E. Elkholi, Olfat Ali Hammam, Mona Magdy, Joan Allalunis-Turner, Marwan Emara
Summary: Myoglobin is expressed in various cancers and is regulated by low oxygen tensions, especially in brain tumors. The expression of myoglobin is positively correlated with tumor grade in brain tumors, suggesting a role in promoting aggressive tumor phenotypes. Enhanced nuclear LDHA expression in GBM also indicates a potential role in tumor aggressiveness.
FRONTIERS IN ONCOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Rocio Villa, Susana Nieto, Antonio Donaire, Pedro Lozano
Summary: Direct biocatalytic processes for CO2 capture and transformation are effective tools for reducing greenhouse gas concentration. Carbonic anhydrase and formate dehydrogenase are two key enzymes that facilitate CO2 uptake and conversion into valuable chemicals.
Article
Biochemistry & Molecular Biology
Joanna A. Quaye, Giovanni Gadda
Summary: Pseudomonas aeruginosa uses D-2-hydroxyglutarate dehydrogenase (PaD2HGDH) to couple the oxidation of D-2-hydroxyglutarate (D2HG) to L-serine biosynthesis for survival. Knockout of PaD2HGDH hinders the growth of P. aeruginosa, making it a potential therapeutic target. This study investigates the metal composition and role of metal as an activator or cofactor for PaD2HGDH.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Jialong Shen, Sonja Salmon
Summary: Innovative carbon capture technologies are needed to combat climate change, including technologies that can capture CO2 from large sources and directly from the air. The captured CO2 can be converted into valuable chemical feedstocks and products, replacing fossil-based materials for a renewable economy. The use of biocatalytic membranes, which combine high reaction rates and enzyme selectivity, shows promise for both capturing and utilizing CO2. This review examines technologies under development that employ enzymes and membranes for CO2 capture and utilization, discussing progress, challenges, and future research directions.
Article
Multidisciplinary Sciences
Ming-Ju Amy Lyu, Udo Gowik, Steve Kelly, Sarah Covshoff, Julian M. Hibberd, Rowan F. Sage, Martha Ludwig, Gane Ka-Shu Wong, Peter Westhoff, Xin-Guang Zhu
Summary: The study on the evolutionary trajectory of C-4 photosynthesis in the Flaveria genus revealed consistent modification patterns in gene expression, protein sequence, and morphological features, with the greatest modifications occurring between C-3-C-4 and C-4-like species. The results support major evolutionary events during the evolution of C-4 metabolism.
SCIENTIFIC REPORTS
(2021)
Article
Endocrinology & Metabolism
Javier Garcia-Bermudez, Michael A. Badgley, Sheela Prasad, Lou Baudrier, Yuyang Liu, Konnor La, Mariluz Soula, Robert T. Williams, Norihiro Yamaguchi, Rosa F. Hwang, Laura J. Taylor, Elisa de Stanchina, Bety Rostandy, Hanan Alwaseem, Henrik Molina, Dafna Bar-Sagi, Kivanc Birsoy
Summary: This study reveals that pancreatic tumor cells overcome aspartate limitation in hypoxia by upregulating macropinocytosis.
Article
Plant Sciences
Abir U. Igamberdiev, Natalia Bykova
Summary: In photosynthetic tissues, chloroplasts are responsible for energy production, while mitochondrial metabolism adjusts to maintain ATP supply and optimize key metabolic fluxes.In the presence of light, the tricarboxylic acid cycle transforms into a noncyclic open structure, supported by the exchange of malate and citrate between chloroplasts and the cytosol. This exchange supports redox energy transfer, contributes to amino acid biosynthesis, and drives secondary metabolism through substrate supply. The coordinated operation of noncoupled mitochondrial respiration and the malate and citrate valves ensures efficient respiration and photorespiration, maintaining redox and energy balance in photosynthetic cells.
Article
Evolutionary Biology
Abir U. Igamberdiev
Summary: The goal of biological evolution is achieved by anticipating and attaining a self-maintaining and adaptable final state of the system. During individual development, biological systems maximize their energy through synergistic effects and become efficient in performing external work. Major evolutionary transitions are achieved through codepoiesis, where undecided statements in existing coding systems form the basis for assigning new values. The complexity in evolution leads to increased power and the ability to perform more external work.
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2023)
Article
Biology
Abir U. Igamberdiev, Leszek A. Kleczkowski
Summary: The general structure of metabolism involves the reproduction of catalysts that control metabolism. This structure achieves autopoiesis and efficient causation, maintaining and operating catalysts through free nucleotides and synthesizing them via encoded information in RNA and DNA polymers. The dual function of ATP, GTP, UTP, and CTP as both free nucleotides and carriers of genetic information affects bioenergetic pathways and nucleic acid turnover. This concept of metabolic closure explains the self-generation and transformative capacity of living systems from prebiotic emergence, based on the duality of nucleotide coenzymes as energetic and informational molecules.
Editorial Material
Plant Sciences
Natalia V. Bykova, Christof Rampitsch, Abir U. Igamberdiev
JOURNAL OF PLANT PHYSIOLOGY
(2023)
Article
Plant Sciences
Leszek A. Kleczkowski, Abir U. Igamberdiev
Summary: Free magnesium ions serve as a powerful signal derived from the interconversion of adenylates. Adenylate kinase (AK) plays a role in equilibrating adenylates and using specific forms of Mg-complexed and Mg-free adenylates. In addition, other reversible Mg2+-dependent enzymes equilibrate non-adenylate nucleotides. AK activity is closely linked to the activities of these enzymes, establishing main hubs for equilibration of non-adenylate nucleotides with Mg2+ controlling the ratios of Mg-chelated and Mg-free nucleotides. This coupling has consequences for various cellular pathways and nucleotide availability for RNA and DNA synthesis.
JOURNAL OF PLANT PHYSIOLOGY
(2023)
Editorial Material
Biochemistry & Molecular Biology
Weibiao Liao, Abir U. Igamberdiev, Jose M. Palma
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Alexander T. Eprintsev, Dmitry N. Fedorin, Abir U. Igamberdiev
Summary: This study investigated the expression and methylation of promoters of genes encoding succinate dehydrogenase, fumarase, and NAD-malate dehydrogenase in maize leaves under different light conditions. The expression of succinate dehydrogenase genes was suppressed by red light and restored by far-red light, accompanied by changes in promoter methylation. The expression of fumarase was regulated by red and far-red light through promoter methylation. Only one gene encoding the mitochondrial NAD-malate dehydrogenase was regulated by light, while the other gene was not affected, and both genes were not controlled by promoter methylation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Robert D. Hill, James de Castro, Mohammed M. Mira, Abir U. Igamberdiev, Kim H. Hebelstrup, Sylvie Renault, Wayne Xu, Ana Badea, Claudio Stasolla
Summary: Oxygen deprivation in the root due to waterlogging affects the growth and productivity of barley. This study investigated the leaf-specific transcriptional responses of waterlogged barley plants and found that over-expression of HvPgb1 enhanced plant resilience to excess moisture and improved photosynthetic rate.
JOURNAL OF PLANT PHYSIOLOGY
(2023)
Article
Plant Sciences
Mohammed M. Mira, Robert D. Hill, Alexander Hilo, Matthias Langer, Sean Robertson, Abir U. Igamberdiev, Olivia Wilkins, Hardy Rolletschek, Claudio Stasolla
Summary: Preservation of stem cell functionality during hypoxia is achieved through the activation of the TCA cycle and the retention of starch and carbohydrates by phytoglobin. Maize QC stem cells, despite being highly hypoxic under normal oxygen tension, are vulnerable to hypoxic stress and show impairment in various metabolic processes. Overexpression of PHYTOGLOBIN 1 preserves the functionality of QC stem cells during stress by rewiring their metabolism.
Article
Biochemistry & Molecular Biology
Eman A. El-Khateeb, Mohamed S. Youssef, Mohammed M. Mira, Abir U. Igamberdiev, Robert D. Hill, Claudio Stasolla
Summary: Oxygen deprivation caused by waterlogging reduces crop productivity, including the oil-producing crop Brassica napus L. This study investigated the early responses of B. napus plants to waterlogging by over-expressing or down-regulating class 1 (BnPgb1) and class 2 (BnPgb2) phytoglobins (Pgbs). Suppression of BnPgb1 exacerbated the decrease in gas exchange parameters and plant biomass, while suppression of BnPgb2 had no effect. Over-expression of BnPgb1 attenuated waterlogging symptoms and activated the antioxidant system and transcriptional induction of folic acid (FA), which could contribute to plant tolerance to waterlogging stress.
Article
Biology
Abir U. Igamberdiev
Summary: The code paradigm in biological and social sciences has its origins in Aristotle's notion of reflexive self-awareness in sense perception. This process generates codes that represent sensory events and constrain human behavior. Coding systems grow through the generation of hypertextual statements, resulting in the establishment of higher-level codes and forming the semiotic screen shared by communicating agents. The emergence of reflexive codes is dependent on a sufficiently complex nervous system and the presence of mirror neurons.
Article
Biochemistry & Molecular Biology
Lilian Vincis Pereira Sanglard, Ian D. Small, Catherine Colas des Francs-Small, Abir U. Igamberdiev
Summary: Researchers created a library of redesigned PPR proteins, related to restorer-of-fertility proteins, and transformed them into plants to target mitochondrial transcripts. Testing 90 different variants in vivo showed a wide range of phenotypes. One specific variant from the library induced specific cleavage of atp1 transcripts, resulting in a phenotype characterized by slow growth and downward curled leaves, validating the use of this library as a source of mitochondrial "mutants". This study is a step towards developing specific RNA targeting tools using PPR proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Plant Sciences
Pradeep Kumar Pathak, Nidhi Yadav, Vemula Chandra Kaladhar, Rekha Jaiswal, Aprajita Kumari, Abir U. Igamberdiev, Gary J. Loake, Kapuganti Jagadis Gupta
Summary: A key feature in the establishment of symbiosis between plants and microbes is the maintenance of the balance between the production and scavenging of nitric oxide (NO). Plant hemoglobins play a central role in scavenging NO and maintaining NO homeostasis. Recent studies have shown that plant hemoglobin 1 is also essential in the establishment and maintenance of plant-bacterial and plant-fungal symbiosis in roots. The classification of plant hemoglobins into symbiotic and non-symbiotic groups is becoming less justified.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Plant Sciences
Robert D. Hill, Abir U. Igamberdiev, Claudio Stasolla
Summary: The preservation of stem cell integrity in hypoxic roots by phytoglobins is achieved through their ability to scavenge nitric oxide and attenuate its effects on auxin transport and cell degradation.
Article
Biology
Abir U. Igamberdiev
Summary: Biological systems strive to maximize self-maintenance and adaptability by establishing stable non-equilibrium states that organize the fluxes of matter and energy and control metabolic processes. These states are realized in autopoietic structures that operate based on biological codes. The principle of thermodynamic buffering optimizes metabolic fluxes, and in developing systems, the principle transforms into increasing external work. Bauer's concept of the stable non-equilibrium state places thermodynamics within the framework of internal biological causality, providing a relational theory of biological thermodynamics.
Article
Biology
Abir U. Igamberdiev, Richard Gordon
Summary: The open process of evolution in multicellular organisms is driven by the rearrangement and growth of the differentiation program. The final stable state of a developmental system determines the direction of evolution and is achieved through a series of differentiation events represented as differentiation trees. Electromechanical signals, acting as a morphogenetic code, play a role in gene expression and contribute to the evolutionary process. The incorporation of mitochondria in eukaryotic cells led to active metabolism and the establishment of a differentiation code, fueling evolution. The invention of continuing differentiation distinguishes multicellular eukaryotes from other organisms. Control mechanisms involving differentiation waves and mechanical consequences of cell differentiations are instrumental in morphogenesis and the achievement of functional stable states. Duplications of differentiation tree branches serve as the basis for continuing differentiation and macroevolution.
