Article
Geriatrics & Gerontology
Jordan D. Fuqua, Marcus M. Lawrence, Zachary R. Hettinger, Agnieszka K. Borowik, Parker L. Brecheen, Marcelina M. Szczygiel, Claire B. Abbott, Frederick F. Peelor, Amy L. Confides, Michael Kinter, Sue C. Bodine, Esther E. Dupont-Versteegden, Benjamin F. Miller
Summary: The failure of old muscle to fully recover after disuse is due to impaired protein folding and degradation mechanisms, rather than limitations in protein synthesis.
JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE
(2023)
Article
Multidisciplinary Sciences
Andrew D. Hanson, Donald R. McCarty, Christopher S. Henry, Xiaochen Xian, Jaya Joshi, Jenelle A. Patterson, Jorge D. Garcia-Garcia, Scott D. Fleischmann, Nathan D. Tivendale, A. Harvey Millar
Summary: Metabolic engineering utilizes enzymes to construct biosystems for specific tasks, with the working life and failure modes of enzymes being important indicators of engineering performance. By adopting catalytic cycles until replacement (CCR) as a metric, the functional lifespan of enzymes in vivo can be calculated, with enzymes in different organisms showing varying CCR values. Enzymes susceptible to damage by specific substrates, products, or mechanisms tend to have shorter lifespans, suggesting that enzyme engineering to increase CCR and reduce replacement costs could be beneficial.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Plant Sciences
Hui Cao, Owen Duncan, A. Harvey Millar
Summary: The study shows a spatiotemporal pattern to protein turnover rates during wheat grain development, and calculates the costs of protein turnover along with identifying the most and the least stable proteins in the developing wheat grain.
Article
Biochemistry & Molecular Biology
Anayat Bhat, Shuang Li, Daniel Hammler, Martin J. Winterhalder, Andreas Marx, Andreas Zumbusch
Summary: The hydrolysis of nucleotides is important for cellular energy, and the transfer of phosphates to proteins is crucial for post-translational modification. A novel fluorogenic adenosine 5'-tetraphosphate (Ap4) analog has been developed for real-time monitoring of ATP hydrolysis within live cells, with potential applications in studying cellular processes involving Ap4 hydrolysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Nutrition & Dietetics
Imogen Hall, Alex Pinto, Sharon Evans, Anne Daly, Catherine Ashmore, Suzanne Ford, Sharon Buckley, Anita MacDonald
Summary: It has not been systematically studied whether adults or caregivers of children with PKU can calculate protein exchanges from food labels on manufactured foods and any difficulties they encounter in interpreting food labels. This study collected data from individuals with PKU or their caregivers about their experience when calculating protein exchanges from food labelling on prepackaged foods. The study found that 31% of respondents found it difficult to interpret food protein exchanges from food labels, and the main issues were non-specificity of protein content, inclusion of protein sources in zero protein foods, and unclear indication of protein content in terms of cooked or uncooked weight.
Article
Biochemistry & Molecular Biology
Sampath K. Gollapudi, Ming Yu, Qing-Fen Gan, Suman Nag
Summary: The study demonstrates that myosin in STFs can mimic the electrostatic and cooperative interactions underlying the energy-sparing SRX state, providing insights into pathophysiological insults and drug interventions. STFs serve as a valuable tool in understanding myosin SRX state in different conditions.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Physics, Multidisciplinary
Matthew P. Leighton, David A. Sivak
Summary: Molecular machines composed of coupled subsystems transduce free energy between different external reservoirs, in the process internally transducing energy and information. While subsystem efficiencies of these molecular machines have been measured in isolation, less is known about how they behave in their natural setting when coupled together and acting in concert. Here, we derive upper and lower bounds on the subsystem efficiencies of a bipartite molecular machine. We demonstrate their utility by estimating the efficiencies of the Fo and F1 subunits of ATP synthase and that of kinesin pulling a diffusive cargo.
PHYSICAL REVIEW LETTERS
(2023)
Article
Medicine, General & Internal
Dana B. Mukamel, Debra Saliba, Heather Ladd, R. Tamara Konetzka
Summary: This study emphasizes the importance of reporting daily variation in staffing to improve understanding of the relationship between staffing and quality in nursing homes. The findings suggest that daily variations in staffing have a significant impact on the quality and ranking of resident care. Measures of daily staffing may enhance the value of Nursing Home Care Compare for quality improvement and consumers searching for high-quality nursing homes.
Article
Biochemistry & Molecular Biology
Sami Chu, Joseph M. Muretta, David D. Thomas
Summary: The study aimed to test whether the IHM structure is the structural basis for the SRX state, and the results indicated that the IHM structure is sufficient but not necessary to produce the SRX kinetic state.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Cell Biology
Kaiming Cao, Shixuan Li, Yu Wang, Hongze Hu, Sijia Xiang, Qianling Zhang, Yangzhong Liu
Summary: Recently, it has been discovered that bacterial cells contain membrane-less organelles formed by liquid-liquid phase separation of proteins or nucleic acids. In this study, it was found that the bacterial nickel-responsive regulatory protein, NikR, exhibits liquid-liquid phase separation in both solution and cells. Furthermore, disrupting the phase separation promotes the expression of nickel transporter genes, suggesting that the formation of these membrane-less compartments is a regulatory mechanism in bacterial cells.
Article
Biochemistry & Molecular Biology
Rosa Merlo, Rosanna Mattossovich, Marianna Genta, Anna Valenti, Giovanni Di Mauro, Alberto Minassi, Riccardo Miggiano, Giuseppe Perugino
Summary: Self-labelling protein tags (SLPs) are versatile tools for sensor imaging that can be genetically fused with any protein of interest. Through computational and structural approaches, a thermostable CLIP-tag named SsOGT-MC8 was developed, which can covalently react with specific substrates at high temperatures.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Medicine, Research & Experimental
Zhen Wang, Dingpeng Zhang, Xinya Hemu, Side Hu, Janet To, Xiaohong Zhang, Julien Lescar, James P. Tam, Chuan-Fa Liu
Summary: Bio-orthogonal tandem ligation using two asparaginyl peptide ligases with differential substrate specificities is a straightforward approach for the preparation of multifunctional protein biologics as potential theranostics.
Article
Chemistry, Organic
Petri A. Turhanen
Summary: The chemical synthesis of the dideuterium-labelled ATP analogue ApppI(d2) is described, and its purification and characterization by various techniques are reported. The quantitative measurement of ApppI in biological samples is of great importance for the study of related diseases.
BEILSTEIN JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Hannah R. R. Belsham, Hanan M. M. Alghamdi, Nikita Dave, Alexandra J. J. Rathbone, Bill Wickstead, Claire T. T. Friel
Summary: The kinesin-13 family consists of microtubule depolymerizing kinesins that play crucial roles in regulating microtubule length. A synthetic ancestral kinesin-13 motor domain was created to better understand the evolution of microtubule depolymerization activity. This study found that the ancestral kinesin-13 motor depolymerizes stabilized microtubules faster than any previously tested depolymerase, suggesting that kinesin-13 family members have evolved to provide more controlled microtubule depolymerization activity.
Article
Biochemistry & Molecular Biology
Ting Luo, Julia Malo Pueyo, Khadija Wahni, Charlotte Yvanoff, Tamas Lazar, Sebastien Pyr dit Ruys, Didier Vertommen, Daria Ezerin, Joris Messens
Summary: Hydrogen peroxide acts as a signaling molecule by oxidizing cysteine thiols in proteins, and recent studies have shown the role of cytosolic peroxiredoxins in transmitting this oxidation to target proteins. Two thiol-disulphide independent in-cell trapping methods, BioID and crosslinker co-immunoprecipitation, coupled with mass spectrometry were used to identify interaction partners of Prdx2, with BioID proving to be a more reliable method. The study identified 13 interactors under elevated H2O2 conditions, including CSN5, and demonstrated the potential of BioID in identifying Prdxs interactors.
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
Biochemistry & Molecular Biology
Sergio Bordel, Diego Martin-Gonzalez, Raul Munoz, Fernando Santos-Beneit
Summary: This study reports the genome of Bacillus altitudinis B12, a bacterium that efficiently degrades PLA and keratin. The genome analysis revealed the presence of genes encoding keratinase and PLA depolymerase, which explain the biodegradation capability of the strain. This bacterium has potential applications in environmentally friendly biotechnology.
MOLECULAR GENETICS AND GENOMICS
(2023)
Article
Multidisciplinary Sciences
Johan Gustafsson, Mihail Anton, Fariba Roshanzamir, Rebecka Jornsten, Eduard J. Kerkhoven, Jonathan L. Robinson, Jens Nielsen
Summary: Single-cell RNA sequencing combined with genome-scale metabolic models has the potential to unravel metabolism differences across cell types and cell states. This study develops a method for generating cell-type-specific models and evaluates the impact of RNA-Seq normalization methods on model topology. The approach successfully detects unique metabolic profiles and cancer-associated differences.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Fernando Santos-Beneit, Le Min Chen, Sergio Bordel, Raquel Frutos de la Flor, Octavio Garcia-Depraect, Raquel Lebrero, Sara Rodriguez-Vega, Raul Munoz, Rosa Aragao Borner, Tim Borner
Summary: In recent years, microbial enzymes capable of degrading plastics have been discovered. Biocatalytic depolymerization mediated by enzymes has emerged as a more efficient and eco-friendly alternative for plastic treatment and recycling. However, the systematic study of depolymerase enzymes in degrading a range of plastic polymers is still lacking.
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
Biochemistry & Molecular Biology
Lucas Coppens, Tanya Tschirhart, Dagmar H. Leary, Sophie M. Colston, Jaimee R. Compton, William Judson Hervey, Karl L. Dana, Gary J. Vora, Sergio Bordel, Rodrigo Ledesma-Amaro
Summary: This study presents the first genome-scale metabolic model (GSMM) of V. natriegens, which was validated and compared with empirical data. The model was used for a metabolic comparison between V. natriegens and Escherichia coli, leading to the discovery of the model architecture of V. natriegens' respiratory and ATP-generating system as well as a sodium-dependent oxaloacetate decarboxylase pump. The proteomics data also provided insights into the halophilic adaptations of V. natriegens. Additionally, a Resource Balance Analysis model was created using the GSMM to study carbon resource allocation.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Monika Pankeviciute-Bukauskiene, Valeryia Mikalayeva, Vaidotas Zvikas, V. Arvydas Skeberdis, Sergio Bordel
Summary: A pipeline for metabolomics was used to test malignant and non-malignant breast cancer cell lines, and an integrated analysis of metabolomics and transcriptomics was carried out. Metabolomics revealed changes in metabolite concentration associated with malignancy, including depleted metabolites and increased serine and pyroglutamic acid. Transcriptomics analysis showed lower expression of the AHCY gene and overexpression of PHGDH, PSPH, and CHAC1 genes in cancer cell lines.
Article
Multidisciplinary Sciences
Min Chen, Tingting Xie, Huan Li, Yingping Zhuang, Jianye Xia, Jens Nielsen
Summary: Supply and regulation of Gibbs free energy and precursors in cellular metabolism are essential for cellular function. In this study, we used multi-omics data under different conditions to investigate the regulation of central carbon metabolism (CCM) in yeast. We identified a metabolism-specific CCM flux regulation mechanism, which is affected by posttranslational modification and allosteric regulation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Genetics & Heredity
Victoria R. Carr, Solon P. Pissis, Peter Mullany, Saeed Shoaie, David Gomez-Cabrero, David L. Moyes
Summary: The diversity of microbial insertion sequences, which are important in generating diversity in microbial genomes, is currently not well represented in microbial databases. In this study, a bioinformatics pipeline called Palidis is introduced to rapidly identify insertion sequences in metagenomic data from mixed microbial communities. Applying Palidis to 264 human metagenomes reveals 879 unique insertion sequences, with 519 being previously unknown. Querying this catalogue against a large database of isolate genomes provides evidence of horizontal gene transfer events across bacterial classes. The development of the Insertion Sequence Catalogue will be continued to serve as a valuable resource for researchers studying insertion sequences in microbial genomes.
MICROBIAL GENOMICS
(2023)
Article
Microbiology
Diego Martin-Gonzalez, Sergio Bordel, Fernando Santos-Beneit
Summary: In this study, efficient chicken feather-degrading Streptomyces bacteria were isolated from honeybee samples. Co-cultivation of these bacteria showed an increase in antibiotic production and metabolic wealth. The production of specialized metabolites was enhanced in co-culture conditions, leading to improved antimicrobial activity against Staphylococcus aureus.
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.