Article
Mathematical & Computational Biology
Amit Kugler, Karin Stensjo
Summary: Understanding energy and redox homeostasis, as well as carbon partitioning, is crucial for systems metabolic engineering of cell factories. Stoichiometric metabolic modeling and network-wide analysis revealed that the rate of NAD(P)H regeneration controls the ATP/NADPH ratio, and energy and redox balance is interconnected with carbon and nitrogen metabolism. An auxiliary pathway was also identified to support cellular redox homeostasis and ATP cycling.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2023)
Article
Plant Sciences
Parveen Akhtar, Avratanu Biswas, Fanny Balog-Vig, Ildiko Domonkos, Laszlo Kovacs, Petar H. Lambrev
Summary: Cyanobacterial mutants with monomeric PSI show changes in the composition and abundance of phycobilisomes and in the excitation energy transfer to PSII and PSI. The oligomeric state of PSI impacts the excitation energy flow in Synechocystis.
Article
Biochemical Research Methods
Ian Sofian Yunus, Zhixuan Wang, Pachara Sattayawat, Jonathan Muller, Fessehaye W. Zemichael, Klaus Hellgardt, Patrik R. Jones
Summary: The study focused on improving the productivity of 1-octanol by enhancing enzyme efficiency and optimizing environmental conditions. By adjusting the inducer concentration and light intensity, the researchers were able to increase the 1-octanol productivity significantly, reaching a carbon partitioning rate of 35% and a titer of 526 mg/L within 12 days.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Kateryna Kukil, Elias Englund, Nick Crang, Elton P. Hudson, Pia Lindberg
Summary: In this study, phenylalanine resistant mutant strains of the unicellular cyanobacterium Synechocystis sp. PCC 6803 were generated by laboratory evolution. The mutant strains were able to secrete phenylalanine and showed potential for production of trans-cinnamic acid and para-coumaric acid. The PRM8 strain demonstrated the highest specific production of these compounds.
METABOLIC ENGINEERING
(2023)
Article
Engineering, Chemical
Tao Sun, Shubin Li, Guangsheng Pei, Lei Chen, Weiwen Zhang
Summary: Synthetic biology research has utilized photosynthetic cyanobacteria as autotrophic cell factories for the direct biosynthesis of various biofuels from CO2. However, the low tolerance to toxicity of biofuels restricts the economic application of cyanobacterial hosts. This study investigates the stress responses of Synechocystis sp. PCC 6803 to exogenous n-hexane using RNAseq transcriptomics and identifies a regulatory gene, slr0724, involved in n-hexane tolerance. This research contributes to a better understanding of cellular responses to n-hexane and the potential engineering of n-hexane tolerance in cyanobacteria.
CHINESE JOURNAL OF CHEMICAL ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Shiqi Lin, Shiliang Li, Tong Ouyang, Gu Chen
Summary: Excess ammonium causes toxicity and stress in cyanobacteria, and how cyanobacteria respond to ammonium stress is not well understood. In this study, a gene called Slr1821 was found to be a crucial regulator for ammonium stress response in Synechocystis sp. PCC6803. The expression of many genes involved in nitrogen uptake, assimilation, and carbon regulation depended on the presence of Slr1821, highlighting its importance in maintaining carbon/nitrogen balance under high nitrogen conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Chen Xu, Bing Wang, Lin Yang, Lucas Zhongming Hu, Lanxing Yi, Yaxuan Wang, Shenglan Chen, Andrew Emili, Cuihong Wan
Summary: In this study, using co-fractionation coupled with LC-MS/MS, the researchers identified 291 multi-protein complexes and 24,092 protein-protein interactions in Synechocystis sp. PCC 6803. These interactions reveal the roles of photosynthesis in various physiological processes and highlight the differences in protein functions between bacteria and higher plants.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Microbiology
Jin Ding, Nils Schuergers, Heike Baehre, Annegret Wilde
Summary: This study discovered functional CARF-domain effector and ring nuclease proteins in the cyanobacterium Synechocystis sp. PCC 6803. The Csx1 homolog, SyCsx1, is a strict cytosine-specific RNase that depends on cyclic tetraadenylate (cA4). Another CARF-domain protein similar to Csm6 effectors, SyCsm6, does not have RNase activity but can degrade cOAs and attenuate SyCsx1 RNase activity. This research suggests that the CRISPR systems in Synechocystis have a multi-layered cA4-mediated defense mechanism.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Plant Sciences
Xiang Li, Chunling Xue, Hui Chen, Huafeng Zhang, Qiang Wang
Summary: This study discovered a small antisense RNA gene (ThfR) that interacts with the thf1 gene, regulating photosynthesis under nitrogen starvation or high-light stress, and enhancing the growth ability of cyanobacteria under high-light stress.
JOURNAL OF PLANT PHYSIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Eunice A. Ferreira, Catarina C. Pacheco, Joao S. Rodrigues, Filipe Pinto, Pedro Lamosa, David Fuente, Javier Urchueguia, Paula Tamagnini
Summary: This study successfully produced glycine betaine using the cyanobacterium Synechocystis sp. PCC 6803 as a chassis, through the construction of synthetic devices in mutant strains.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Lucas Gewehr, Benedikt Junglas, Ruven Jilly, Johannes Franz, Wenyu Eva Zhu, Tobias Weidner, Mischa Bonn, Carsten Sachse, Dirk Schneider
Summary: The dynamin-like protein SynDLP in the cyanobacterium Synechocystis sp. PCC 6803 forms ordered oligomers and interacts with negatively charged thylakoid membrane lipids independently of nucleotides. The structural characteristics of SynDLP suggest it to be a bacterial ancestor of eukaryotic dynamin.
NATURE COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Eleftheria-Angeliki Valsami, Angeliki Pateraki, Anastasios Melis, Demetrios F. Ghanotakis
Summary: This study investigated various cultivation conditions for heterologous beta-phellandrene production by Synechocystis sp. PCC 6803, finding that immobilized cells in calcium alginate beads resulted in higher production compared to suspended cultures. Additionally, extreme conditions of pH 10.5 and 600 mM NaCl proved to be conducive for cell growth and beta-phellandrene production, offering new approaches for sustainable production of terpenoids.
JOURNAL OF APPLIED PHYCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Vetaka Tharasirivat, Saowarath Jantaro
Summary: The overexpression of the RuBisCO gene can increase cyanobacterial biomass and improve biocompound production. We successfully constructed two strains of Synechocystis sp. PCC 6803 that overexpressed the rbc gene, resulting in faster growth compared to the wild type strain. The increased biomass of these strains led to higher production of polyhydroxybutyrate (PHB) under nutrient-deprived conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Environmental Sciences
Gang Ruan, Wujuan Mi, Xuwang Yin, Gaofei Song, Yonghong Bi
Summary: This study investigated the physiological response of Synechocystis sp. PCC 6803 to cadmium stress and identified the toxicity targets and response mechanisms. Cadmium was found to damage the cell's photosynthesis and ultrastructure. The study also identified the target sites of cadmium and revealed that the upregulation of the ABC transporter pathway and its protein expression contributed to the response mechanism to cadmium toxicity.
Article
Plant Sciences
Shoki Ito, Atsuko Watanabe, Takashi Osanai
Summary: This study biochemically characterized the L-aspartate oxidase from Synechocystis sp. PCC 6803 and determined its role in NADP+ biosynthesis under photoautotrophic conditions. The results provide important insights into the regulatory mechanism of cyanobacterial NADP+ biosynthesis.
Review
Dentistry, Oral Surgery & Medicine
Taihiko Yamaguchi, Saki Mikami, Masana Maeda, Taishi Saito, Toshinori Nakajima, Wataru Yachida, Akihito Gotouda
Summary: This article reviews the current state of portable/wearable EMG devices for assessment of bruxism. The results show that ultra-miniaturized wearable EMG devices with performance equivalent to conventional devices have been developed and used during sleep and in the daytime, with a high level of diagnostic accuracy for sleep bruxism. However, a definite cut-off value for awake bruxism has not been established.
CRANIO-THE JOURNAL OF CRANIOMANDIBULAR & SLEEP PRACTICE
(2023)
Article
Biochemistry & Molecular Biology
Feiran Li, Yu Chen, Mihail Anton, Jens Nielsen
Summary: Enzyme parameters are crucial for understanding, modeling, and engineering cells. Experimental measurements only cover a small portion of enzyme-compound pairs, and even less in non-model organisms. Artificial intelligence techniques have accelerated the exploration of enzyme properties by predicting them in a high-throughput manner. GotEnzymes is a comprehensive database that provides predicted enzyme parameters using AI approaches, allowing for interactive web exploration and programmatic access.
NUCLEIC ACIDS RESEARCH
(2023)
Editorial Material
Biotechnology & Applied Microbiology
Gen Zou, Jens B. Nielsen, Yongjun Wei
Summary: Recent advances in synthetic biology have revolutionized mushroom farming by shifting the focus from traditional cultivation to comprehensive applications using cutting-edge biotechnologies. Promising applications in this field include precision breeding, exploration of biosynthetic gene clusters, development of mushroom chassis cells, and construction of cell factories for high-value products.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Nutrition & Dietetics
Umberto Maria Battisti, Chunixa Gao, Fady Akladios, Woonghee Kim, Hong Yang, Cemil Bayram, Ismail Bolat, Metin Kiliclioglu, Nursena Yuksel, Ozlem Ozdemir Tozlu, Cheng Zhang, Jihad Sebhaoui, Shazia Iqbal, Saeed Shoaie, Ahmet Hacimuftuoglu, Serkan Yildirim, Hasan Turkez, Mathias Uhlen, Jan Boren, Adil Mardinoglu, Morten Grotli
Summary: This study presents a new finding that ellagic acid and its derivatives can selectively and potently inhibit liver pyruvate kinase, which may open up new therapeutic options for non-alcoholic fatty liver disease (NAFLD).
Article
Neurosciences
Burak Yulug, Ozlem Altay, Xiangyu Li, Lutfu Hanoglu, Seyda Cankaya, Simon Lam, Halil Aziz Velioglu, Hong Yang, Ebru Coskun, Ezgi Idil, Rahim Nogaylar, Ahmet Ozsimsek, Cemil Bayram, Ismail Bolat, Sena Oner, Ozlem Ozdemir Tozlu, Mehmet Enes Arslan, Ahmet Hacimuftuoglu, Serkan Yildirim, Muhammad Arif, Saeed Shoaie, Cheng Zhang, Jens Nielsen, Hasan Turkez, Jan Boren, Mathias Uhlen, Adil Mardinoglu
Summary: A clinical trial was conducted to study the effect of combined metabolic activators (CMA) on Alzheimer's disease (AD) patients. The results showed that CMA can improve cognitive functions and clinical parameters associated with AD. This study provides evidence for the use of CMA in the treatment of AD.
TRANSLATIONAL NEURODEGENERATION
(2023)
Article
Mathematical & Computational Biology
Bouchra Ezzamouri, Dorines Rosario, Gholamreza Bidkhori, Sunjae Lee, Mathias Uhlen, Saeed Shoaie
Summary: The human gut microbiome plays a significant role in metabolic disorders, such as type 2 diabetes mellitus. This study investigates the mechanistic role of the gut microbiome in response to metformin treatment, using metagenomics data and genome-scale metabolic modeling. The results demonstrate the commensal and competing behavior of key bacterial species in response to metformin and highlight the impact of different nutritional environments.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2023)
Article
Biochemical Research Methods
Le Yuan, Hongzhong Lu, Feiran Li, Jens Nielsen, Eduard J. Kerkhoven
Summary: In this study, a computational toolbox called HGTphyloDetect was developed, which combines high-throughput analysis with phylogenetic inference to accurately identify horizontal gene transfer (HGT) events and illustrate the transmission pathway among evolutionarily distant or closely related species. The HGTphyloDetect toolbox is user-friendly, capable of detecting HGT events with high efficiency and low false discovery rate.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Andreas Hober, Mirela Rekanovic, Bjorn Forsstrom, Sara Hansson, David Kotol, Andrew J. Percy, Mathias Uhlen, Jan Oscarsson, Fredrik Edfors, Tasso Miliotis
Summary: This study presents a novel quantitative approach to determine the absolute concentration of apo(a) in two microliters of plasma using proteotypic peptides, which meets the requirements for targeted proteomics assays. The assay parameters were optimized, and the LC-SRM/MS results were compared with a commercially available immunoassay.
Article
Multidisciplinary Sciences
Leo Dahl, Ilana B. Kotliar, Annika Bendes, Tea Dodig-Crnkovic, Samuel Fromm, Arne Elofsson, Mathias Uhlen, Thomas P. Sakmar, Jochen M. Schwenk
Summary: A multiplexed immunoassay was developed to test the selectivity of over 400 anti-GPCR antibodies. The results showed that about 61% of the antibodies were selective, 11% bound off-target, and 28% did not bind to any GPCR. It was also found that on-target antibodies had longer, more disordered antigens and were less buried in the interior of GPCR proteins compared to other antibodies.
Editorial Material
Endocrinology & Metabolism
Hong Yang, Cheng Zhang, Hasan Turkez, Mathias Uhlen, Jan Boren, Adil Mardinoglu
Review
Biotechnology & Applied Microbiology
Mathias Uhlen, Stephen R. Quake
Summary: The impact of next-generation sequencing (NGS) is of great significance in the field of life science, contributing to our understanding of human health, disease, biology, and ecology. The majority of NGS systems are based on the concept of 'sequencing by synthesis' (SBS), which uses engineered DNA polymerase for sequential detection of nucleotide incorporation. This review discusses some key concepts leading to the development of NGS technology.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Chemistry, Analytical
Ivana Bardino Novosel, Anina Ritterband-Rosenbaum, Georgios Zampoukis, Jens Bo Nielsen, Jakob Lorentzen
Summary: This study developed and trained an image-based Convolutional Neural Network (CNN) to recognize specific movement classifiers relevant to individuals with cerebral palsy (CP). Monitoring and quantifying movement behavior in CP patients using multiple wearable sensors and CNN is of great value for improving their health outcomes.
Article
Materials Science, Multidisciplinary
Morteza Aghaee, Arun Akkala, Zulfi Alam, Rizwan Ali, Alejandro Alcaraz Ramirez, Mariusz Andrzejczuk, Andrey E. Antipov, Pavel Aseev, Mikhail Astafev, Bela Bauer, Jonathan Becker, Srini Boddapati, Frenk Boekhout, Jouri Bommer, Tom Bosma, Leo Bourdet, Samuel Boutin, Philippe Caroff, Lucas Casparis, Maja Cassidy, Sohail Chatoor, Anna Wulf Christensen, Noah Clay, William S. Cole, Fabiano Corsetti, Ajuan Cui, Paschalis Dalampiras, Anand Dokania, Gijs de Lange, Michiel de Moor, Juan Carlos Estrada Saldana, Saeed Fallahi, Zahra Heidarnia Fathabad, John Gamble, Geoff Gardner, Deshan Govender, Flavio Griggio, Ruben Grigoryan, Sergei Gronin, Jan Gukelberger, Esben Bork Hansen, Sebastian Heedt, Jesus Herranz Zamorano, Samantha Ho, Ulrik Laurens Holgaard, Henrik Ingerslev, Linda Johansson, Jeffrey Jones, Ray Kallaher, Farhad Karimi, Torsten Karzig, Cameron King, Maren Elisabeth Kloster, Christina Knapp, Dariusz Kocon, Jonne Koski, Pasi Kostamo, Peter Krogstrup, Mahesh Kumar, Tom Laeven, Thorvald Larsen, Kongyi Li, Tyler Lindemann, Julie Love, Roman Lutchyn, Morten Hannibal Madsen, Michael Manfra, Signe Markussen, Esteban Martinez, Robert McNeil, Elvedin Memisevic, Trevor Morgan, Andrew Mullally, Chetan Nayak, Jens Nielsen, William Hvidtfelt Padkaer Nielsen, Bas Nijholt, Anne Nurmohamed, Eoin OFarrell, Keita Otani, Sebastian Pauka, Karl Petersson, Luca Petit, Dmitry I. Pikulin, Frank Preiss, Marina Quintero-Perez, Mohana Rajpalke, Katrine Rasmussen, Davydas Razmadze, Outi Reentila, David Reilly, Richard Rouse, Ivan Sadovskyy, Lauri Sainiemi, Sydney Schreppler, Vadim Sidorkin, Amrita Singh, Shilpi Singh, Sarat Sinha, Patrick Sohr, Tomas Stankevic, Lieuwe Stek, Henri Suominen, Judith Suter, Vicky Svidenko, Sam Teicher, Mine Temuerhan, Nivetha Thiyagarajah, Raj Tholapi, Mason Thomas, Emily Toomey, Shivendra Upadhyay, Ivan Urban, Saulius Vaitiekenas, Kevin Van Hoogdalem, David Van Woerkom, Dmitrii V. Viazmitinov, Dominik Vogel, Steven Waddy, John Watson, Joseph Weston, Georg W. Winkler, Chung Kai Yang, Sean Yau, Daniel Yi, Emrah Yucelen, Alex Webster, Ruichen Zhao
Summary: In this study, measurements and simulations of semiconductor-superconductor heterostructure devices were conducted to observe topological superconductivity and Majorana zero modes. The devices were optimized to ensure robustness against nonuniformity and disorder. Experimental results indicate the presence of a topological superconducting phase, which is a prerequisite for experiments involving Majorana zero modes fusion and braiding.