Article
Biochemistry & Molecular Biology
Irene Dervisi, Kosmas Haralampidis, Andreas Roussis
Summary: AtRD19c is a papain-like cysteine protease known for its participation in anther development and interaction with AtSBP1. Its gene expression is regulated by selenium and it localizes in the root tip, lateral roots, and leaf trichomes. The physical interaction with AtSBP1 was confirmed through BiFC in planta.
Article
Biotechnology & Applied Microbiology
Felix Sigmund, Oleksandr Berezin, Sofia Beliakova, Bernhard Magerl, Martin Drawitsch, Alberto Piovesan, Filipa Goncalves, Silviu-Vasile Bodea, Stefanie Winkler, Zoe Bousraou, Martin Grosshauser, Eleni Samara, Jesus Pujol-Marti, Sebastian Schaedler, Chun So, Stephan Irsen, Axel Walch, Florian Kofler, Marie Piraud, Joergen Kornfeld, Kevin Briggman, Gil Gregor Westmeyer
Summary: By incorporating metal-interacting moieties into encapsulin nanocompartments, researchers created a suite of electron microscopy-readable barcodes called EMcapsulins. These barcodes can be automatically segmented and differentiated, and their coding capacity can be increased by arranging them into distinct patterns. EMcapsulins are compatible with different types of electron microscopy techniques and can provide multiplexed gene expression maps. They have been successfully applied to brain imaging.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Kai Chen, Weican Liu, Xiaowei Li, Haiyan Li
Summary: GmGASA32, a member of the GASA family, is regulated by gibberellin and affects soybean height. Experimental verification of GmGASA32 response to gibberellin and its function in the nucleus were conducted in this study.
PLANT SIGNALING & BEHAVIOR
(2021)
Article
Plant Sciences
Daniel Luedke, Charlotte Roth, Sieglinde A. Kamrad, Jana Messerschmidt, Denise Hartken, Jonas Appel, Bojan F. Hoernich, Qiqi Yan, Stefan Kusch, Melanie Klenke, Annette Gunkel, Lennart Wirthmueller, Marcel Wiermer
Summary: IMPORTIN-alpha 3/MOS6 is a key factor in regulating immune responses in Arabidopsis, primarily responsible for the nuclear transport of SNC1, playing an important role in autoimmunity and basal disease resistance.
Article
Environmental Sciences
Jose Cavalcante Souza Vieira, Camila Pereira Braga, Joao Vitor de Queiroz, Bruna Cavecci-Mendonca, Grasieli de Oliveira, Natalia Galvao de Freitas, Ana Angelica Henrique Fernandes, Mileni da Silva Fernandes, Marilia Afonso Rabelo Buzalaf, Jiri Adamec, Luiz Fabricio Zara, Pedro de Magalhaes Padilha
Summary: Exposure to mercury can interfere with protein and enzyme expression, compromise important pathways, and induce metallothionein expression. The study found that two predatory fish species had higher concentrations of mercury in their tissues compared to a non-carnivorous species. The presence of mercury was identified in protein spots, and metal-binding proteins were identified as possible biomarkers of mercury exposure in fish.
Article
Biochemistry & Molecular Biology
Irene Dervisi, Orfeas Petropoulos, Adamantia Agalou, Varvara Podia, Nikolaos Papandreou, Vassiliki A. Iconomidou, Kosmas Haralampidis, Andreas Roussis
Summary: In this study, we investigated the role of AtSAH7, a member of the Ole e 1 domain-containing family, in Arabidopsis thaliana. We discovered a novel interaction between AtSAH7 and Selenium-binding protein 1 (AtSBP1). Our results showed that the minimal promoter for AtSAH7 is located 1420 bp upstream of the transcription start site and is responsible for inducing expression in vasculature tissues. Furthermore, we found that AtSAH7 expression is acutely increased under selenite treatment in response to oxidative stress, suggesting its involvement in a selenite-regulated biochemical network associated with ROS production.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Evolutionary Biology
Filip Cervenak, Regina Sepsiova, Jozef Nosek, Lubomir Tomaska
Summary: Telomeres in eukaryotic species protect the ends of nuclear chromosomes, with diverse telomeric repeat sequences across different species. The evolutionary origin and co-evolutionary mechanisms between telomeric repeats and telomere-binding proteins remain unclear.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Jeongjin J. Kim, Mohammed E. Sayed, Alexander Ahn, Aaron L. Slusher, Jeffrey Y. Ying, Andrew T. Ludlow
Summary: This study identified a NOVA1-PTBP1-PTBP2 axis that regulates TERT alternative splicing (AS) in iPSCs and their differentiation into NPCs. It also found that splice-switching of TERT, which regulates telomerase activity, is induced by different cell densities in stem cells but not cancer cells. These findings are important for developing telomerase inhibition-based cancer therapies that reduce damage to stem cells.
Review
Environmental Sciences
Lihui Zhao, Miaomiao Teng, Xiaoli Zhao, Yunxia Li, Jiaqi Sun, Wentian Zhao, Yuefei Ruan, Kenneth M. Y. Leung, Fengchang Wu
Summary: Legacy per- and polyfluoroalkyl substances (PFASs) have raised concerns due to their widespread presence in the environment and potential hazards to wildlife and human health. Although there are increasing numbers of effective PFAS alternatives, these alternatives also pose new challenges. This paper reviews how PFASs bind to transport proteins, nuclear receptors, and membranes, and discusses the variations in affinity for endogenous proteins introduced by structural features of PFAS alternatives. The toxic effects and mechanisms of action of legacy PFASs can be compared with their alternatives using binding models, and future studies should integrate in vitro experiments and in silico quantitative structure-activity relationship modeling for better toxicity predictions.
ENVIRONMENT INTERNATIONAL
(2023)
Editorial Material
Multidisciplinary Sciences
Lori Frappier
Summary: A protein called EBNA1 from Epstein-Barr virus has been proven to bind to and break human chromosome 11, resulting in genomic instability that might contribute to cancer susceptibility.
Article
Chemistry, Physical
Casey Weisenberger, David Hathcock, Michael Hinczewski
Summary: The section discusses the accurate propagation of signals through stochastic biochemical networks and regulatory mechanisms for suppressing fluctuations in biomolecular populations. Despite limitations in applying Wiener-Kolmogorov optimal noise filter theory to nonlinear signaling systems, it is still considered an excellent approximation tool for predicting performance limits in biological systems.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Cell Biology
Yan Li, Na Zhang, Chao Ma, Wenwen Xu, Guiyuan Jin, Yi Zheng, Lei Zhang, Bingyu Liu, Chengjiang Gao, Suxia Liu
Summary: Tipe2 may have a dual function in regulating cellular senescence, suppressing tumor cell proliferation and survival while promoting tumorigenesis initiation under exposure to dangerous environments such as AOM/DSS-related inflammation.
CELL DEATH & DISEASE
(2021)
Article
Chemistry, Inorganic & Nuclear
Jaeick Lee, Rosemary A. Dalton, Arnaud Basle, Nicolas Vita, Christopher Dennison, Bacillus Subtilis
Summary: A family of bacterial copper storage proteins, known as Csps, have been studied. Different homologues of Csps with potentially different Cu(I)-binding properties have been identified. A new subgroup of Csp3s has been discovered, with the crystal structure of RkCsp3 from Methylocystis sp. strain Rockwell being the first studied example. This new subgroup has structural differences from classical Csp3s, but exhibits rapid Cu(I) binding and removal.
INORGANIC CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Inna Armandari, Walderik W. Zomerman, Sabine L. A. Plasschaert, Marlinde J. Smit, Tosca E. Martini, Eduardo S. de Camargo Magalhaes, Shanna M. Hogeling, Geesina C. Rozema-Huizinga, Harm J. Lourens, Tiny G. J. Meeuwsen-de Boer, Frank J. G. Scherpen, Eveline S. J. M. de Bont, Sophia W. M. Bruggeman
Summary: The study found that phosphorylation of the transcription factor CREB correlates strongly with survival in medulloblastoma patients and differentiation phenotype. During normal cerebellar development, phosphorylated CREB is selectively expressed in differentiating cerebellar granule neuron progenitor cells. Inducing CREB activation via PKA-mediated signaling enhances sensitivity of medulloblastoma cells to chemotherapy.
SCIENTIFIC REPORTS
(2021)
Review
Chemistry, Multidisciplinary
Shankar Mandal, Zi Li, Tanmay Chatterjee, Kunal Khanna, Karen Montoya, Liuhan Dai, Chandler Petersen, Lidan Li, Muneesh Tewari, Alexander Johnson-Buck, Nils G. Walter
Summary: Current methods for detecting disease biomarkers in biofluids face challenges such as insufficient analytical performance and high cost. SiMREPS, an amplification-free approach, overcomes these challenges by providing high specificity and sensitivity for detecting diverse biomarkers. Early proof-of-concept studies have shown its effectiveness in detecting miRNAs and rare mutant DNA alleles with high specificity and single-molecule sensitivity.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Jana Fulneckova, Ladislav Dokladal, Karolina Kolarova, Martina Nespor Dadejova, Klara Prochazkova, Sabina Gomelska, Martin Sivcak, Katerina Adamusova, Martin Lycka, Vratislav Peska, Martina Dvorackova, Eva Sykorova
Summary: This study explores the interaction network of Arabidopsis telomerase proteins with nucleosome assembly proteins and the minichromosome maintenance system, providing new insights into telomerase functions related to telomere chromatin assembly and replication. By investigating 176 candidate proteins, numerous interactions during telomerase biogenesis were identified, shedding light on the complex network of telomerase interactions. Additionally, the study identified protein domains responsible for binding and analyzed the subcellular localization of these interactions, offering a comprehensive view of telomerase contacts with multiprotein complexes involved in chromatin remodeling and cell differentiation pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Nutrition & Dietetics
Saira Ambreen, Sameen Fatima, Ahmed Elwakiel, Rajiv Rana, Kunal Singh, Anubhuti Gupta, Dheerendra Gupta, Hamzah Khawaja, Jayakumar Manoharan, Christian Besler, Ulrich Laufs, Shrey Kohli, Berend Isermann, Khurrum Shahzad
Summary: Diabetes mellitus is associated with accelerated atherosclerosis and impaired plaque stability, with reduced TM expression and aPC generation. Impaired TM function reduces plaque stability, a characteristic of hyperglycemia-associated plaques, suggesting the crucial role of impaired TM function in mediating diabetes-associated atherosclerosis.
Article
Nutrition & Dietetics
Sameen Fatima, Saira Ambreen, Akash Mathew, Ahmed Elwakiel, Anubhuti Gupta, Kunal Singh, Shruthi Krishnan, Rajiv Rana, Hamzah Khawaja, Dheerendra Gupta, Jayakumar Manoharan, Christian Besler, Ulrich Laufs, Shrey Kohli, Berend Isermann, Khurrum Shahzad
Summary: High glucose-induced maladaptive unfolded protein response and associated senescence promote vascular endothelial cell dysfunction, which can be reversed by activated protein C.
Article
Nutrition & Dietetics
Rajiv Rana, Jayakumar Manoharan, Anubhuti Gupta, Dheerendra Gupta, Ahmed Elwakiel, Hamzah Khawaja, Sameen Fatima, Silke Zimmermann, Kunal Singh, Saira Ambreen, Ihsan Gadi, Ronald Biemann, Shihai Jiang, Khurrum Shahzad, Shrey Kohli, Berend Isermann
Summary: Diabetic kidney disease (DKD) is a growing pandemic associated with obesity and diabetes mellitus. DKD is now the leading cause of end-stage renal disease and is linked to increased risk of cardiovascular morbidity and mortality. This study demonstrates that the cytoprotective coagulation protease activated protein C (aPC) reduces mitochondrial ROS generation in tubular cells and mitigates renal sterile inflammation in DKD, supporting the potential therapeutic use of aPC in DKD treatment.
Article
Nutrition & Dietetics
Silke Zimmermann, Mandy Vogel, Akash Mathew, Thomas Ebert, Rajiv Rana, Shihai Jiang, Berend Isermann, Ronald Biemann
Summary: The study investigated the impact of lifestyle-induced weight loss (LIWL) intervention on prediabetes and metabolic syndrome, and found that a greater initial weight loss can reduce the risk of recurrence of these diseases.
Article
Multidisciplinary Sciences
Moh'd Mohanad Al-Dabet, Khurrum Shahzad, Ahmed Elwakiel, Alba Sulaj, Stefan Kopf, Fabian Bock, Ihsan Gadi, Silke Zimmermann, Rajiv Rana, Shruthi Krishnan, Dheerendra Gupta, Jayakumar Manoharan, Sameen Fatima, Sumra Nazir, Constantin Schwab, Ronny Baber, Markus Scholz, Robert Geffers, Peter Rene Mertens, Peter P. Nawroth, John H. Griffin, Maria Keller, Chris Dockendorff, Shrey Kohli, Berend Isermann
Summary: One major obstacle in diabetes is the hyperglycemic memory, which lacks specific therapies. In diabetic kidney disease (DKD), glucose-mediated changes in gene expression persist even after reversing hyperglycemia. The gene p21, associated with the p53-p21 pathway, is found to be consistently induced by hyperglycemia and linked to DKD severity. The sustained expression of p21 in DKD is associated with demethylation of its promoter and reduced DNMT1 expression. Two disease resolving agents, 3K3A-aPC and parmodulin-2, can reverse the sustained p21 expression, tubular senescence, and DKD, highlighting p21 as a potential therapeutic target for hyperglycemic memory in DKD.
NATURE COMMUNICATIONS
(2022)
Article
Plant Sciences
Bozena Klodova, David Potesil, Lenka Steinbachova, Christos Michailidis, Ann-Cathrin Lindner, Dieter Hackenberg, Jorg D. Becker, Zbynek Zdrahal, David Twell, David Honys
Summary: This study provides a comprehensive investigation into the gene expression dynamics in developing Arabidopsis pollen by integrating RNA and proteomic data. The findings identify potential regulatory factors, changes in alternative splicing, and provide insights into mRNA translation rate and storage, laying the foundation for further studies on the role of alternative splicing in this model.
PLANT REPRODUCTION
(2022)
Review
Genetics & Heredity
Leon P. Jenner, Vratislav Peska, Jana Fulneckova, Eva Sykorova
Summary: Telomeres are essential structures in most eukaryotes formed from satellite DNA repeats at the ends of chromosomes. The role of satellite DNA repeat sequences in the eukaryotic cell remains enigmatic, with ongoing research needed to fully understand their biological function, especially in non-model organisms. This review aims to inspire and facilitate new research into telomeres and satellites, emphasizing accessible experimental and in silico methods, using examples from plants and insects to expand beyond traditional human and yeast models.
Article
Biochemistry & Molecular Biology
Petr Fajkus, Matej Adamik, Andrew D. L. Nelson, Agata M. Kilar, Michal Franek, Michal Bubenik, Radmila Capkova Frydrychova, Alena Votavova, Eva Sykorova, Jiri Fajkus, Vratislav Peska
Summary: Unlike the catalytic subunit of telomerase, the RNA subunit (TR) shows significant differences in size, sequence and biogenesis across eukaryotes. Previous views assumed a common origin of TRs transcribed with RNA polymerase II in Opisthokonta and Trypanosomida, and TRs transcribed with RNA polymerase III in TSAR and Archaeplastida. However, new findings from studying Hymenoptera TRs challenge this assumption and suggest an evolutionary switch in TR type and biogenesis that is associated with the divergence of Arthropods.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Klara Prikrylova Konecna, Agata Kilar, Petra Kovacikova, Jiri Fajkus, Eva Sykorova, Miloslava Fojtova
Summary: This study investigates the interaction between ARM and telomerase and explores the cellular functions of ARM. The results show that ARM is involved in crucial cellular processes and has a dominant effect. Additionally, ARM is implicated in circadian rhythms and responses to drugs and stimuli.
Article
Plant Sciences
Eva Dvorak Tomastikova, Fen Yang, Kristina Mlynarova, Said Hafidh, Sarka Schorova, Alzbeta Kusova, Marketa Pernisova, Tereza Prerovska, Bozena Klodova, David Honys, Jiri Fajkus, Ales Pecinka, Petra Prochazkova Schrumpfova
Summary: RUVBL1 and RUVBL2 are crucial for the proper development of male and female gametophytes in Arabidopsis. Mutations in these genes result in abnormal embryo sac structure and nuclear numbers. The expression of these proteins is observed in pollen grains, embryo sac, and tapetum cells, playing important roles in reproductive development.
Correction
Plant Sciences
Bozena Klodova, David Potesil, Lenka Steinbachova, Christos Michailidis, Ann-Cathrin Lindner, Dieter Hackenberg, Jorg D. Becker, Zbynek Zdrahal, David Twell, David Honys
PLANT REPRODUCTION
(2023)
Article
Cell Biology
Jonathan A. Lindquist, Anja Bernhardt, Charlotte Reichardt, Eva Sauter, Sabine Brandt, Rajiv Rana, Maja T. Lindenmeyer, Lars Philipsen, Berend Isermann, Cheng Zhu, Peter R. Mertens
Summary: DNA-binding protein A (DbpA), a member of the Y-box family, plays a role in transcription and translation by binding and regulating mRNA. In a mouse model of kidney disease, DbpA expression was induced in the renal interstitium. Deficiency of the Ybx3 gene resulted in protection against tissue injury and reduced immune cell infiltration and extracellular matrix deposition. Our RNAseq data showed that Ybx3 is expressed by activated fibroblasts in the renal interstitium. These findings suggest that targeting DbpA may be a potential therapeutic option for slowing down kidney disease progression.
Article
Hematology
Dheerendra Gupta, Ahmed Elwakiel, Satish Ranjan, Manish Kumar Pandey, Shruthi Krishnan, Saira Ambreen, Reinhard Henschler, Rajiv Rana, Maria Keller, Uta Ceglarek, Khurrum Shahzad, Shrey Kohli, Berend Isermann
Summary: Recent research has shown that the coagulation protease activated protein C (aPC) can directly regulate adaptive immunity. Preincubation of T cells with aPC before transplantation increases FOXP3+ regulatory T cells (Tregs) and reduces acute graft-versus host disease (aGVHD) in mice, but the mechanism behind this is unknown. This study found that cellular metabolism plays a role in aPC-induced FOXP3+ expression in T cells, specifically through a decrease in glutamine and α-ketoglutarate levels, resulting in altered epigenetic markers, promoter demethylation, and induction of FOXP3 expression. These findings suggest that aPC modulates T-cell metabolism to promote a Treg-like phenotype.
Correction
Biochemistry & Molecular Biology
Ravinder Nagpal, Pradip Behare, Rajiv Rana, Ashwani Kumar, Manoj Kumar, Sanu Arora, Francesco Marotta, Shalini Jain, Hariom Yadav
Summary: Correction for the article 'Bioactive peptides derived from milk proteins and their health beneficial potentials: an update' by Ravinder Nagpal et al., Food Funct., 2011, 2, 18-27, DOI: 10.1039/C0FO00016G. The correction provides an update on the health beneficial potentials of bioactive peptides derived from milk proteins.