Article
Chemistry, Multidisciplinary
Noa Avidan, Michael Levy, Shirley S. Daube, Roy H. Bar-Ziv
Summary: We compartmentalize cascaded gene expression reactions in a DNA brush, starting from cell-free synthesis of a unidirectional recombinase that exchanges information between two DNA molecules. Recombination yield in the DNA brush is responsive to gene composition, density, and orientation, with faster kinetics than in a homogeneous dilute bulk solution reaction. The ability to encode the DNA recombinase in the same DNA brush with its substrate constructs enables multiple spatially resolved orthogonal recombination transactions.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Cell Biology
Jonghee Han, Junho Hyun, Jaesang Park, Sunmin Jung, Yoonseo Oh, Youbin Kim, Shin-Hyeon Ryu, Seo-Hyun Kim, Eun Il Jeong, Dong-Gyu Jo, Sung-Hye Park, Yong-Keun Jung
Summary: PKM2 functions as a positive regulator of gamma-secretase, promoting the production of A beta in AD and exacerbating impairment of spatial and recognition memory.
Article
Pharmacology & Pharmacy
Brittney H. Davis, T. Mark Beasley, Michelle Amaral, Jerzy P. Szaflarski, Tyler Gaston, Leslie Perry Grayson, David G. Standaert, E. Martina Bebin, Nita A. Limdi
Summary: This study found that genetic variations are associated with CBD response in TRE patients, influencing the expression of CBD targets and revealing potential drug interactions. The results highlight the important role of pharmacogenes in treatment resistance.
CLINICAL PHARMACOLOGY & THERAPEUTICS
(2021)
Review
Plant Sciences
Xinwei Wang, Yaqi An, Pan Xu, Jianwei Xiao
Summary: Pentatricopeptide repeat (PPR) proteins are one of the largest nuclear-encoded protein families in higher plants, with over 400 members in most sequenced plant species. They play an important role in the post-transcriptional regulation of chloroplast and mitochondrial genes, affecting the biogenesis and functioning of both organelles and influencing plant photosynthesis, respiration, and development.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemical Research Methods
Alma Andersson, Joakim Lundeberg
Summary: In this study, a novel method was proposed to analyze spatial transcriptomics data, which simulated the diffusion of individual transcripts to extract genes with spatial patterns, generating satisfactory results on synthetic and real data. Compared to existing methods, this approach seemed to be less influenced by gene expression levels and showed better time performance when run with multiple cores.
Article
Engineering, Environmental
Hengliang Huang, Mei Li, Muhammad Rizwan, Zhihua Dai, Yuan Yuan, Md Muzammel Hossain, Menghua Cao, Shuanglian Xiong, Shuxin Tu
Summary: Silicon and selenium can effectively alleviate cadmium toxicity in rice plants, with a strong synergistic effect when used together. Their interaction mainly occurs through regulating gene expression, sequestering Cd in root cell walls and organelles, and reducing Cd transfer to shoots.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Multidisciplinary Sciences
Yulia Kargapolova, Rizwan Rehimi, Huelya Kayserili, Joanna Bruehl, Konstantinos Sofiadis, Anne Zirkel, Spiros Palikyras, Athanasia Mizi, Yun Li, Goekhan Yigit, Alexander Hoischen, Stefan Frank, Nicole Russ, Jonathan Trautwein, Bregje van Bon, Christian Gilissen, Magdalena Laugsch, Eduardo Gade Gusmao, Natasa Josipovic, Janine Altmueller, Peter Nuernberg, Gernot Laengst, Frank J. Kaiser, Erwan Watrin, Han Brunner, Alvaro Rada-Iglesias, Leo Kurian, Bernd Wollnik, Karim Bouazoune, Argyris Papantonis
Summary: Members of the CHD chromatin remodeler family are implicated in human pathologies, however CHD6 remained poorly studied. Here, the authors show that CHD6 binds to and regulates autophagy and stress response genes across cell types. They identify a clinical mutation that affects its ability to recruit cofactors, leading to impaired autophagy induction and DNA repair.
NATURE COMMUNICATIONS
(2021)
Article
Engineering, Environmental
Gaoxiang Huang, Changfeng Ding, Naijia Guo, Mingjun Ding, Hua Zhang, Muhammad Kamran, Zhigao Zhou, Taolin Zhang, Xingxiang Wang
Summary: The study found that coating manganese can significantly reduce cadmium uptake by rice, particularly by inhibiting root absorption and internal transportation. The addition of lime increases soil pH and reduces extractable cadmium, but also decreases soil dissolved manganese, affecting cadmium control in rice. The combined addition of lime and coated manganese can effectively reduce cadmium content in rice.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Multidisciplinary Sciences
Shizhe Yu, Haoren Wang, Lingpeng Yang, Yingxue Yan, Qiang Cai, Duo Ma, Long Jiang, Zehai Gao, Zhiyong Yu, Zongping Xia
Summary: The comprehensive study of the spatial-cellular anatomy of the human liver is crucial for understanding the cellular origins of liver disease. In this study, spatial transcriptomics were conducted on normal human liver tissue sections, providing detailed transcriptional information on liver zonation. A total of 6581 high-quality spots from normal livers were analyzed, mainly consisting of hepatocytes, which were classified into four sub-groups. These data serve as a reliable reference for studying the spatial heterogeneity of liver lobules.
Article
Plant Sciences
Lars H. Kruse, Benjamin Fehr, Jason D. Chobirko, Gaurav D. Moghe
Summary: This study provides insights into the functional evolution and prediction of the BAHD acyltransferase family in flowering plants. The expansion of BAHDs in land plants is associated with significant changes in gene features, and different plant groups exhibit clade expansions related to specific metabolite classes. Co-expression analysis and metabolic pathway models contribute to the recovery of metabolic processes and novel functional predictions for BAHD acyltransferases.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Chemistry, Medicinal
Kristaps Berzins, Reinis Muiznieks, Matiss R. Baumanis, Inese Strazdina, Karlis Shvirksts, Santa Prikule, Vytautas Galvanauskas, Daniel Pleissner, Agris Pentjuss, Mara Grube, Uldis Kalnenieks, Egils Stalidzans
Summary: Docosahexaenoic acid (DHA) is an important long-chain polyunsaturated fatty acid with numerous health benefits. Crypthecodinium cohnii, a marine dinoflagellate, is used for industrial production of DHA due to its ability to accumulate high concentrations of DHA. Glycerol, a by-product of biodiesel production and other industries, is found to be a potential substrate for DHA production. Comparative analysis of glycerol, ethanol, and glucose as substrates for DHA production shows that glycerol has the slowest biomass growth rate but the highest fraction of PUFAs, particularly DHA.
Review
Biochemistry & Molecular Biology
Shir Bahiri-Elitzur, Tamir Tuller
Summary: Codon usage bias refers to the differing frequencies of synonymous codons in genes and organisms, believed to be a balance between mutational biases and natural selection. Various codon usage bias indices have been developed to estimate the fitness of coding sequences to different phenomena, with applications in biomedical fields. Despite the differences in aims, many indices tend to correlate, highlighting the importance of continuously developing new indices to capture additional aspects of gene expression steps.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Cell Biology
Yongjia Wang, Yuqin Zhang, Zixuan Wang, Lu Yu, Keli Chen, Yuwen Xie, Yang Liu, Weijie Liang, Yilin Zheng, Yizhi Zhan, Yi Ding
Summary: NUPR1 is overexpressed in hepatocellular carcinoma and is associated with poor prognosis. NUPR1 overexpression correlates with highly proliferative and aggressive phenotype of HCC cells. Inhibition of NUPR1 may be a therapeutic alternative for hepatocellular carcinoma.
CELL DEATH DISCOVERY
(2022)
Article
Multidisciplinary Sciences
Eszter Zavodszky, Sew-Yeu Peak-Chew, Szymon Juszkiewicz, Ana J. Narvaez, Ramanujan S. Hegde
Summary: In eukaryotic cells, excess PSMC5, a subunit of the proteasome base, is targeted for degradation by the HERC1 ubiquitin ligase. HERC1 recognizes unassembled PSMC5 with the help of its assembly chaperone PAAF1 and can also engage in the degradation of later assembly intermediates such as the PSMC4-PSMC5-PAAF1 complex. A missense mutant of HERC1 impairs the recognition and ubiquitination of the PSMC5-PAAFI complex, indicating that proteasome assembly factors can serve as adaptors for ubiquitin ligases to eliminate unassembled intermediates and maintain protein homeostasis.
Article
Multidisciplinary Sciences
Guoxin Cui, Migle K. Konciute, Lorraine Ling, Luke Esau, Jean -Baptiste Raina, Baoda Han, Octavio R. Salazar, Jason S. Presnell, Nils Raedecker, Huawen Zhong, Jessica Menzies, Phillip A. Cleves, Yi Jin Liew, Cory J. Krediet, Val Sawiccy, Maha J. Cziesielski, Paul Guagliardo, Jeremy Bougoure, Mathieu Pernice, Heribert Hirt, Christian R. Voolstra, Virginia M. Weis, John R. Pringle, Manuel Aranda
Summary: Symbiotic cnidarians, such as corals and anemones, have evolved efficient molecular mechanisms for nutrient distribution and recycling in order to thrive in nutrient-poor ocean environments. Using the sea anemone Aiptasia, researchers have discovered that glucose and the presence of algae induce the up-regulation and relocalization of glucose and ammonium transporters, which are critical for symbiont functioning and organism-wide nitrogen assimilation. These findings provide insight into the molecular mechanisms underlying nitrogen conservation and recycling in symbiotic cnidarians.
Article
Medicine, Research & Experimental
Travis Nemkov, Davide Stefanoni, Aarash Bordbar, Aaron Issaian, Bernhard O. Palsson, Larry J. Dumont, Ariel Hay, Anren Song, Yang Xia, Jasmina S. Redzic, Elan Z. Eisenmesser, James C. Zimring, Steve Kleinman, Kirk C. Hansen, Michael P. Busch, Angelo D'Alessandro
Summary: Computational models suggest that mature erythrocytes may be affected by common drugs. High-throughput drug screenings show that many drugs impact erythrocyte metabolism, with machine learning models accurately predicting these effects. Certain drugs like ranitidine can improve erythrocyte metabolism and storage quality, indicating potential for enhancing blood transfusion outcomes.
Article
Microbiology
Prerna Bali, Joanna Coker, Ivonne Lozano-Pope, Karsten Zengler, Marygorret Obonyo
Summary: After infection with H. felis, all genotypes of mice showed a decrease in gastric microbial diversity, with a higher proportion of Lactobacillales potentially related to gastric cancer progression. Differences in genotypes could influence the stomach microbiome, making it more susceptible to developing gastric cancer upon Helicobacter infection.
Article
Biochemical Research Methods
Zachary B. Haiman, Daniel C. Zielinski, Yuko Koike, James T. Yurkovich, Bernhard O. Palsson
Summary: The article introduces the MASSpy package, an open-source computational framework for dynamic modeling of metabolism using mass action kinetics and detailed chemical mechanisms. By adding dynamic modeling tools to the COBRApy package, MASSpy provides a unified framework for constraint-based and kinetic modeling of metabolic networks. MASSpy supports high-performance dynamic simulation using libRoadRunner: the Systems Biology Markup Language (SBML) simulation engine.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Correction
Multidisciplinary Sciences
Woori Kim, Soonkyu Hwang, Namil Lee, Yongjae Lee, Suhyung Cho, Bernhard Palsson, Byung-Kwan Cho
Summary: The paper has been corrected and the details can be found at the provided link.
Article
Microbiology
Soonkyu Hwang, Namil Lee, Donghui Choe, Yongjae Lee, Woori Kim, Yujin Jeong, Suhyung Cho, Bernhard O. Palsson, Byung-Kwan Cho
Summary: In this study, transcriptional regulatory elements in Streptomyces clavuligerus were identified using genome-wide transcript 3'-end positions and transcription units. The study revealed the importance of transcript 3'-end positions in controlling transcription levels and the potential for designing engineering tools to enhance secondary metabolite production based on these findings.
Article
Biochemistry & Molecular Biology
Jean-Christophe Lachance, Dominick Matteau, Joelle Brodeur, Colton J. Lloyd, Nathan Mih, Zachary A. King, Thomas F. Knight, Adam M. Feist, Jonathan M. Monk, Bernhard O. Palsson, Pierre-Etienne Jacques, Sebastien Rodrigue
Summary: Mesoplasma florum, a fast-growing near-minimal organism, was used as a model to explore rational genome designs and construct the iJL208 metabolic model. Through this work, a rational approach to genome design was established, laying the groundwork for model-driven whole-genome engineering.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ye Gao, Hyun Gyu Lim, Hans Verkler, Richard Szubin, Daniel Quach, Irina Rodionova, Ke Chen, James T. Yurkovich, Byung-Kwan Cho, Bernhard O. Palsson
Summary: This study experimentally evaluated 40 uncharacterized proteins in Escherichia coli, confirming 34 as DNA-binding proteins and inferring potential functions for 10 of them. The research significantly expanded the number of confirmed TFs, provided putative functions for newly discovered TFs, and confirmed the functions of four representative TFs through mutant phenotypes.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Amir Akbari, James T. Yurkovich, Daniel C. Zielinski, Bernhard O. Palsson
Summary: The study investigates how abiotic constraints shape metabolism in Escherichia coli. It reveals that these constraints are fundamental in driving the evolution of high-affinity phosphate transporters, regulating transcriptional responses to osmotic and acid stress. Understanding these constraints is crucial for comprehending the outcomes of evolutionary adaptation.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Gabriela Canto-Encalada, Diego Tec-Campos, Juan D. Tibocha-Bonilla, Karsten Zengler, Alejandro Zepeda, Cristal Zuniga
Summary: The ammonia-oxidizing bacterium Nitrosomonas europaea plays a significant role in nitrogen cycle and wastewater treatment. Its metabolic versatility and ability to degrade environmental pollutants make it suitable for harsh environmental conditions. The genome-scale metabolic model iGC535 provides quantitative insight into the central and specialized metabolism of N. europaea, particularly in the oxidation of ammonia and pollutant metabolism. The manually curated model can predict phenotypes under different growth conditions and sheds light on the impact of carbon source on key pathways.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Editorial Material
Microbiology
Joanna Coker, Livia S. Zaramela, Karsten Zengler
Summary: Cooperative interaction between low-abundance gut bacteria is essential for converting l-carnitine to TMAO via a multi-step pathway, ultimately leading to an increased risk of cardiovascular disease.
NATURE MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Anurag Passi, Juan D. Tibocha-Bonilla, Manish Kumar, Diego Tec-Campos, Karsten Zengler, Cristal Zuniga
Summary: Genome-scale metabolic models (GEMs) enable the quantitative description of the relationship between genotype and phenotype by integrating different types of Big Data. This review analyzes the available Big Data for metabolic modeling and compiles the GEM reconstruction tools that utilize Big Data. It also discusses the applications of GEMs in industry and research, as well as the future prospects in emerging areas.
Article
Microbiology
Livia S. Zaramela, Megan Tjuanta, Oriane Moyne, Maxwell Neal, Karsten Zengler
Summary: The synthetic DNA (synDNA) spike-ins developed in this study enable accurate and reproducible measurements of the absolute amount and fold changes of bacterial species in complex microbial communities. This versatile and promising method can be applied to bacterial communities or genomic features, with the potential for low-cost adaptation by other research groups. The sequences of the synDNAs and plasmids are made available for future application of this method in the study of microbial communities.
Article
Mathematical & Computational Biology
Juan D. Tibocha-Bonilla, Cristal Zuniga, Asama Lekbua, Colton Lloyd, Kevin Rychel, Katie Short, Karsten Zengler
Summary: Bacillus subtilis, a well-characterized microorganism, has been used as a model for studying Gram-positive bacteria. Metabolic modeling has helped optimize its metabolism for various applications, but traditional models are not suitable for simulating protein production and proteomic response to stress. In this study, a new metabolism and gene expression model (ME-model) of B. subtilis, iJT964-ME, was reconstructed and validated. The model outperformed previous models in predicting gene essentiality and was successfully validated using physiological and omics data. Furthermore, the model identified the mechanism behind the upregulation of tryptophan synthesis under ethanol stress and predicted amylase production rates under different growth conditions.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2022)
Article
Biochemical Research Methods
Diego Tec-Campos, Camila Posadas, Juan D. Tibocha-Bonilla, Deepan Thiruppathy, Nathan Glonek, Cristal Zuniga, Alejandro Zepeda, Karsten Zengler
Summary: The purple non-sulfur bacterium Rhodopseudomonas palustris is recognized for its important role in nitrogen and carbon cycling and its presence in wastewater treatment communities. It is capable of various metabolic processes under different growth conditions and can degrade a wide range of pollutants. However, many of its metabolic mechanisms remain unknown. In this study, a comprehensive metabolic model was developed and validated, enabling a better understanding of R. palustris' metabolic processes in different environments.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Maxwell Neal, Deepan Thiruppathy, Karsten Zengler
Summary: This study developed a genome-scale metabolic model of B. fragilis strain 638R, providing a basis for understanding its relationship with human diet and metabolic products.
PLOS COMPUTATIONAL BIOLOGY
(2023)
