Article
Cardiac & Cardiovascular Systems
Alba Alvarez-Franco, Raquel Rouco, Rafael J. Ramirez, Guadalupe Guerrero-Serna, Maria Tiana, Sara Cogliati, Kuljeet Kaur, Mohammed Saeed, Ricardo Magni, Jose Antonio Enriquez, Fatima Sanchez-Cabo, Jose Jalife, Miguel Manzanares
Summary: Transcriptomic and proteomic analysis of AF progression in a large animal model shows significant changes occurring at early stages, including previously undescribed increase in mitochondria, changes to the chromatin of atrial CMs, and genes related to neural function and cell proliferation.
CARDIOVASCULAR RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Niall Conlon, Richard A. Murphy, Aoife Corrigan, Sean Doyle, Rebecca A. Owens, Sheena Fagan
Summary: This study investigated the effects of yeast and its derivatives on broiler chickens using a quantitative proteomic strategy. The results showed that YCW supplementation provided various beneficial effects, including immune stimulation, changes in oxidative status, stimulation of metabolic processes, and hepatoprotective effects. In addition, specific protein detection may serve as biomarkers for evaluating the efficacy of GHP supplementation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
Xianrong Wong, Jevon A. Cutler, Victoria E. Hoskins, Molly Gordon, Anil K. Madugundu, Akhilesh Pandey, Karen L. Reddy
Summary: The nuclear lamina is a protein network that provides structural and gene regulatory functions. LADs are a large fraction of the mammalian genome that are repressed by their association to the nuclear periphery. By using two different methods, proteins at the nuclear periphery have been identified and essential proteins for LAD function have been discovered.
LIFE SCIENCE ALLIANCE
(2021)
Article
Multidisciplinary Sciences
Carla Ines Soares Rodrigues, Maxime den Ridder, Martin Pabst, Andreas K. Gombert, Sebastian Aljoscha Wahl
Summary: The identity and amount of carbon sources have significant impacts on the growth and physiology of microbial species. This study compared the proteomes of Saccharomyces cerevisiae cells grown on sucrose or glucose as the sole carbon source. Different strains exhibited different physiological responses to sucrose, with some showing higher growth rates on sucrose while others showed the opposite.
SCIENTIFIC REPORTS
(2023)
Article
Biotechnology & Applied Microbiology
Irina Charlot Pena-Moreno, Denise Castro Parente, Karolini Miranda da Silva, Elton Pedro Nunes Pena, Fabiana Aparecida Cavalcante Silva, Tercilio Calsa Junior, Will de Barros Pita, Marcos Antonio de Morais Jr
Summary: The yeast Dekkera bruxellensis exhibits superior anaerobic growth and ethanol yield in the presence of nitrate, due to balanced activation of TORC1 and NCR de-repression mechanisms regulating cell metabolism. On the other hand, poor growth in aerobiosis is likely caused by oxidative stress triggered by nitrate when oxygen is present.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Koji Katsumata, Yuichi Ichikawa, Tomohiro Fuse, Hitoshi Kurumizaka, Akio Yanagida, Takeshi Urano, Hiroaki Kato, Mitsuhiro Shimizu
Summary: Trinucleotide repeat sequences are short repetitive DNA sequences that have an impact on nucleosome formation. Some sequences have the ability to promote nucleosome formation, while others have the ability to exclude nucleosome formation.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Environmental Sciences
Ruben Ferrer Velasco, Melvin Lippe, Fabian Tamayo, Tiza Mfuni, Renezita Sales-Come, Cecilia Mangabat, Thomas Schneider, Sven Guenter
Summary: Tropical forests are shrinking rapidly, posing a threat to their ecosystem services. Despite challenges, a study has developed a method to generate accurate forest maps using remote sensing data.
REMOTE SENSING OF ENVIRONMENT
(2022)
Article
Microbiology
Marcos Abreu Almeida, Lilian Cristiane Baeza, Rodrigo Almeida-Paes, Alexandre Melo Bailao, Clayton Luiz Borges, Allan Jefferson Guimaraes, Celia Maria Almeida Soares, Rosely Maria Zancope-Oliveira
Summary: Histoplasma capsulatum is a globally distributed thermally dimorphic fungus that causes histoplasmosis. The proteomic comparison between its mycelium and yeast cells revealed significant metabolic differences between the two growth forms. Proteins associated with glycolysis and alcoholic fermentation were abundant in mycelium, while proteins related to the tricarboxylic acid cycle and response to temperature stress were predominant in yeast cells.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Francisco Amil-Ruiz, Ana Maria Herruzo-Ruiz, Carlos Fuentes-Almagro, Casimiro Baena-Angulo, Jose Manuel Jimenez-Pastor, Julian Blasco, Jose Alhama, Carmen Michan
Summary: This study focused on analyzing the molecular mechanisms of pollutant responses in the bivalve species Scrobicularia plana by creating a robust reference transcriptome and proteome database. Through a comprehensive approach, a high-quality assembly was selected and proteomic analysis revealed a wide coverage of molecular functions and biological processes, confirming the strength of the generated database.
Article
Multidisciplinary Sciences
Joana Figueiredo, Rita B. Santos, Leonor Guerra-Guimaraes, Celine C. Leclercq, Jenny Renaut, Rui Malho, Andreia Figueiredo
Summary: This study presents the first in-planta proteome characterization of P. viticola, providing insights into its colonization strategy in susceptible and resistant grapevine genotypes.
SCIENTIFIC REPORTS
(2022)
Article
Environmental Studies
Xuecheng Wei, Yang Bai
Summary: The US and China, as major contributors to global CO2 emissions, have made significant efforts but are still far from achieving carbon neutrality and a sustainable environment (SEN). This study compares the roles of natural reserves (NTR) and green financing (GFN) in the US and China using the BARDL technique. The study also validates the relevance of the Environment Kuznets Curve (EKC) in both countries with NTR and GFN. The findings show the incremental effects of NTR on CO2 and the detrimental effects of GFN on CO2, as well as the validation of EKC. Based on the findings, both countries are recommended to preserve the NTR and implement more environmentally friendly initiatives supported by GFN and sustainable investments for ecological improvement.
Article
Geography, Physical
Christin Hilbich, Christian Hauck, Coline Mollaret, Pablo Wainstein, Lukas U. Arenson
Summary: Increasing water scarcity in the Central Andes due to climate change has caused a debate on the significance of permafrost occurrences for the hydrologic cycle. This study presents data from six geophysical campaigns in the Central Andes of Chile and Argentina, showing that ice-rich permafrost is not limited to rock glaciers but also exists in non-rock-glacier permafrost slopes. The study highlights the importance of considering non-rock-glacier permafrost landforms in quantifying the hydrological significance of permafrost.
Article
Public, Environmental & Occupational Health
Jacqueline Nkrumah, Aaron Asibi Abuosi, Rodney Buadi Nkrumah
Summary: In Ghana's Effutu Municipality, healthcare facilities do not provide a breastfeeding-friendly work environment beyond the privileges granted by labor laws and conditions of service. Continuous advocacy for breastfeeding workplace support and stakeholder engagement to establish consensus on suitable strategies are recommended for optimal breastfeeding and increased productivity.
Article
Environmental Sciences
Michaela Doukari, Konstantinos Topouzelis
Summary: This study proposes an efficient methodology for marine habitat mapping using unmanned aerial systems (UAS) and object-based image analysis (OBIA), along with image quality and accuracy assessment. The methodology was tested in four coastal areas in Greece, demonstrating its effectiveness and reliability.
REMOTE SENSING APPLICATIONS-SOCIETY AND ENVIRONMENT
(2022)
Article
Geography, Physical
Mukti Ram Subedi, Carlos Portillo-Quintero, Samanthaa S. Kahl, Nancy E. McIntyre, Robert D. Cox, Gad Perry
Summary: This study presents a geographic object-based image analysis approach using a random forest algorithm to classify large-area land use and land cover. The approach achieves high accuracy in classifying a mosaic of orthoimagery in central Texas by considering the spatial structure of sample data. The study demonstrates a cost-effective way to generate an accurate multi-class land use/land cover map using high-spatial/low-spectral resolution orthoimagery.
PHOTOGRAMMETRIC ENGINEERING AND REMOTE SENSING
(2023)
Article
Urology & Nephrology
Marc Johnsen, Torsten Kubacki, Assa Yeroslaviz, Martin Richard Spaeth, Jannis Moersdorf, Heike Gobel, Katrin Bohl, Michael Ignarski, Caroline Meharg, Bianca Habermann, Janine Altmueller, Andreas Beyer, Thomas Benzing, Bernhard Schermer, Volker Burst, Roman-Ulrich Mueller
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2020)
Article
Biochemistry & Molecular Biology
Annie Yim, Prasanna Koti, Adrien Bonnard, Fabio Marchiano, Milena Duerrbaum, Cecilia Garcia-Perez, Jose Villaveces, Salma Gamal, Giovanni Cardone, Fabiana Perocchi, Zuzana Storchova, Bianca H. Habermann
NUCLEIC ACIDS RESEARCH
(2020)
Article
Microbiology
Friedhelm Pfeiffer, Gerald Losensky, Anita Marchfelder, Bianca Habermann, Mike Dyall-Smith
Article
Biology
Aynur Kaya-Copur, Fabio Marchiano, Marco Y. Hein, Daniel Alpern, Julie Russeil, Nuno Miguel Luis, Matthias Mann, Bart Deplancke, Bianca H. Habermann, Frank Schnorrer
Summary: Research has shown that the regulated activity of core members of the Hippo pathway is necessary for muscle growth, with Dlg5 and Slmap identified as regulators of the STRIPAK phosphatase to enable post-mitotic muscle growth. This pathway controls the timing and levels of sarcomeric gene expression during development, potentially contributing to muscle or cardiomyocyte growth in humans.
Article
Agronomy
Jin-Ho Yun, Michael Pierrelee, Dae-Hyun Cho, Urim Kim, Jina Heo, Dong-Yun Choi, Yong Jae Lee, Bongsoo Lee, HyeRan Kim, Bianca Habermann, Yong Keun Chang, Hee-Sik Kim
Summary: Transcriptome analysis reveals that Chlorella sp. HS2 downregulates photosynthesis and TCA pathways while upregulates DNA repair mechanisms and ABC transporters under high salinity stress. Additionally, the algae reallocates storage carbon towards lipids to alleviate cellular stress caused by ROS and maintain viability.
FOOD AND ENERGY SECURITY
(2021)
Article
Multidisciplinary Sciences
Ziad Al Tanoury, John F. Zimmerman, Jyoti Rao, Daniel Sieiro, Harold M. McNamara, Thomas Cherrier, Alejandra Rodriguez-delaRosa, Aurore Hick-Colin, Fanny Bousson, Charlotte Fugier-Schmucker, Fabio Marchiano, Bianca Habermann, Jerome Chal, Alexander P. Nesmith, Svetlana Gapon, Erica Wagner, Vandana A. Gupta, Rhonda Bassel-Duby, Eric N. Olson, Adam E. Cohen, Kevin Kit Parker, Oliver Pourquie
Summary: This study introduces an in vitro human model to investigate the pathology of Duchenne muscular dystrophy (DMD) and test new therapeutic approaches. The researchers describe an optimized protocol for differentiating human induced pluripotent stem cells (iPSC) to a late myogenic stage, which allows them to replicate classic DMD phenotypes in isogenic DMD-mutant iPSC lines. Treatment with prednisolone significantly improves muscle function in DMD iPSC lines, challenging the prevailing view that its benefits are solely due to anti-inflammatory properties.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Arno Meiler, Fabio Marchiano, Margaux Haering, Michaela Weikunat, Frank Schnorrer, Bianca H. Habermann
Summary: AnnoMiner is an innovative tool for annotating and integrating gene expression regulation data, predicting transcriptional regulators for specific biological processes without requiring chromatin data from the same process.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Michael Pierrelee, Ana Reynders, Fabrice Lopez, Aziz Moqrich, Laurent Tichit, Bianca H. Habermann
Summary: Integrating -omics data with biological networks is an important approach in understanding gene expression changes, and TimeNexus is introduced as a Cytoscape app to project time-series data onto multilayer networks for further analysis. This tool allows researchers to easily create and visualize temporal multilayer networks, and extract relevant cellular pathways and active subnetworks.
SCIENTIFIC REPORTS
(2021)
Article
Biology
Sofiene Seef, Julien Herrou, Paul de Boissier, Laetitia My, Gael Brasseur, Donovan Robert, Rikesh Jain, Romain Mercier, Eric Cascales, Bianca H. Habermann, Tam Mignot
Summary: Myxococcus xanthus, a soil bacterium, preys collectively on prey colonies using A-motility and contact-dependent killing as central predatory mechanisms. The newly discovered Kil-like systems form a new class of Tad-like machineries in predatory bacteria, with a conserved function in predator-prey interactions. This study also reveals a novel cell-cell interaction function for bacterial pili-like assemblages.
Article
Genetics & Heredity
Xavier Caubit, Elise Arbeille, Dorian Chabbert, Florence Desprez, Imane Messak, Ahmed Fatmi, Bianca Habermann, Paolo Gubellini, Laurent Fasano
Summary: This study revealed that Tshz3 is mainly expressed in striatal cholinergic interneurons (SCINs) and can be deleted efficiently by the Camk2a-Cre transgene. The findings help reinterpret experiments using Camk2a-Cre-dependent gene manipulations and provide insights into the cellular and molecular mechanisms underlying ASD-related behavioral abnormalities observed in Tshz3 mouse models.
FRONTIERS IN GENETICS
(2021)
Article
Microbiology
Rikesh Jain, Bianca H. Habermann, Tam Mignot
Summary: Myxococcus xanthus, a Gram-negative social bacterium, is considered crucial for the microbial ecosystem. This study presents a complete high-quality reference genome of the M. xanthus strain DZ2, providing valuable insights into its genetic makeup.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Biochemistry & Molecular Biology
Fabio Marchiano, Margaux Haering, Bianca Hermine Habermann
Summary: Mitochondria, subcellular organelles present in eukaryotic cells, play a central role in cellular metabolism. The upgraded version 2.0 of the mitoXplorer platform provides integrative functions and novel features to help identify regulatory factors of mitochondrial processes and facilitate data analysis.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Qiyan Mao, Achyuth Acharya, Alejandra Rodriguez-delaRosa, Fabio Marchiano, Benoit Dehapiot, Ziad Al Tanoury, Jyoti Rao, Margarete Diaz-Cuadros, Arian Mansur, Erica Wagner, Claire Chardes, Vandana Gupta, Pierre-Francois Lenne, Bianca H. Habermann, Olivier Theodoly, Olivier Pourquie, Frank Schnorrer
Summary: This study investigates the mechanisms of human muscle morphogenesis using an in vitro system with induced pluripotent stem cell-derived human myogenic precursors. The researchers found that mechanical tension plays a key role in coordinating the multi-scale self-organisation of muscle morphogenesis, including sarcomeric components and differentiating myofibers.
Article
Biochemical Research Methods
Maxime Lucas, Arthur Morris, Alex Townsend-Teague, Laurent Tichit, Bianca Habermann, Alain Barrat
Summary: Phasik is an automatic method that identifies the temporal organization of biological systems by combining time series data and interaction data. It builds a (partially) temporal network and uses clustering to infer temporal phases. We demonstrate its effectiveness by studying different phases of the cell cycle and phase arrests of mutants, as well as temporal gene expression data from circadian rhythms in mouse models. This method will be valuable for studying temporal regulation in lesser-known biological contexts as high-resolution multiomics datasets become more common.
CELL REPORTS METHODS
(2023)
Article
Ecology
Amelie Vernale, Maria Mandela Prunster, Fabio Marchiano, Henry Debost, Nicolas Brouilly, Caroline Rocher, Dominique Massey-Harroche, Emmanuelle Renard, Andre Le Bivic, Bianca H. Habermann, Carole Borchiellini
Summary: The study focused on the morphogenic characteristics of the homoscleromorph sponge Oscarella lobularis, revealing conservation of molecular toolkit involved in epithelial features loss and restoration between Homoscleromorpha and Bilateria, suggesting a common role in the last common ancestor of animals. Sponge-specific genes showed differential expression during cell dissociation and reaggregation processes, calling for future functional characterization of these genes.
BMC ECOLOGY AND EVOLUTION
(2021)