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Stefan Golfier, Thomas Quail, Jan Brugués
Single-Molecule Approaches to Study DNA Condensation.
Methods Mol Biol, 2740 1-19 (2024)
PubMed Source   

Proteins drive genome compartmentalization across different length scales. While the identities of these proteins have been well-studied, the physical mechanisms that drive genome organization have remained largely elusive. Studying these mechanisms is challenging owing to a lack of methodologies to parametrize physical models in cellular contexts. Furthermore, because of the complex, entangled, and dense nature of chromatin, conventional live imaging approaches often lack the spatial resolution to dissect these principles. In this chapter, we will describe how to image the interactions of λ-DNA with proteins under purified and cytoplasmic conditions. First, we will outline how to prepare biotinylated DNA, functionalize coverslips with biotin-conjugated poly-ethylene glycol (PEG), and assemble DNA microchannels compatible for the imaging of protein-DNA interactions using total internal fluorescence microscopy. Then we will describe experimental methods to image protein-DNA interactions in vitro and DNA loop extrusion using Xenopus laevis egg extracts.
@article{Golfier8685,
author={Stefan Golfier, Thomas Quail, Jan Brugués},
title={Single-Molecule Approaches to Study DNA Condensation.},
journal ={Methods in molecular biology (Clifton, N.J.)},
volume={2740},
pages={1--19},
year=2024
}

Thorsten Meyer, Oskar Knittelfelder, Martin Smolnig, Patrick Rockenfeller
Quantifying yeast lipidomics by high-performance thin-layer chromatography (HPTLC) and comparison to mass spectrometry-based shotgun lipidomics.
Microb Cell, 11 57-68 (2024)
Open Access PubMed Source Full Text   

Lipidomic analysis in diverse biological settings has become a frequent tool to increase our understanding of the processes of life. Cellular lipids play important roles not only as being the main components of cellular membranes, but also in the regulation of cell homeostasis as lipid signaling molecules. Yeast has been harnessed for biomedical research based on its good conservation of genetics and fundamental cell organisation principles and molecular pathways. Further application in so-called humanised yeast models have been developed which take advantage of yeast as providing the basics of a living cell with full control over heterologous expression. Here we present evidence that high-performance thin-layer chromatography (HPTLC) represents an effective alternative to replace cost intensive mass spectrometry-based lipidomic analyses. We provide statistical comparison of identical samples by both methods, which support the use of HPTLC for quantitative analysis of the main yeast lipid classes.
@article{Meyer8686,
author={Thorsten Meyer, Oskar Knittelfelder, Martin Smolnig, Patrick Rockenfeller},
title={Quantifying yeast lipidomics by high-performance thin-layer chromatography (HPTLC) and comparison to mass spectrometry-based shotgun lipidomics.},
journal ={Microbial cell (Graz, Austria)},
volume={11},
pages={57--68},
year=2024
}

Angela L Caipa Garcia#, Jill E Kucab, Halh Al-Serori, Rebekah S S Beck, Madjda Bellamri, Robert J Turesky, John D Groopman, Hayley E Francies, Mathew J Garnett, Meritxell Huch, Jarno Drost, Matthias Zilbauer, Volker M Arlt, David H Phillips#
Tissue Organoid Cultures Metabolize Dietary Carcinogens Proficiently and Are Effective Models for DNA Adduct Formation.
Chem Res Toxicol, 37(2) 234-247 (2024)
Open Access PubMed Source   

Human tissue three-dimensional (3D) organoid cultures have the potential to reproduce in vitro the physiological properties and cellular architecture of the organs from which they are derived. The ability of organoid cultures derived from human stomach, liver, kidney, and colon to metabolically activate three dietary carcinogens, aflatoxin B1 (AFB1), aristolochic acid I (AAI), and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), was investigated. In each case, the response of a target tissue (liver for AFB1; kidney for AAI; colon for PhIP) was compared with that of a nontarget tissue (gastric). After treatment cell viabilities were measured, DNA damage response (DDR) was determined by Western blotting for p-p53, p21, p-CHK2, and γ-H2AX, and DNA adduct formation was quantified by mass spectrometry. Induction of the key xenobiotic-metabolizing enzymes (XMEs) CYP1A1, CYP1A2, CYP3A4, and NQO1 was assessed by qRT-PCR. We found that organoids from different tissues can activate AAI, AFB1, and PhIP. In some cases, this metabolic potential varied between tissues and between different cultures of the same tissue. Similarly, variations in the levels of expression of XMEs were observed. At comparable levels of cytotoxicity, organoids derived from tissues that are considered targets for these carcinogens had higher levels of adduct formation than a nontarget tissue.
@article{Garcia8655,
author={Angela L Caipa Garcia, Jill E Kucab, Halh Al-Serori, Rebekah S S Beck, Madjda Bellamri, Robert J Turesky, John D Groopman, Hayley E Francies, Mathew J Garnett, Meritxell Huch, Jarno Drost, Matthias Zilbauer, Volker M Arlt, David H Phillips},
title={Tissue Organoid Cultures Metabolize Dietary Carcinogens Proficiently and Are Effective Models for DNA Adduct Formation.},
journal ={Chemical research in toxicology},
volume={37},
issue ={2},
pages={234--247},
year=2024
}

Colette Dehay#, Wieland Huttner#
Development and evolution of the primate neocortex from a progenitor cell perspective.
Development, 151(4) Art. No. dev199797 (2024)
PubMed Source   

The generation of neurons in the developing neocortex is a major determinant of neocortex size. Crucially, the increase in cortical neuron numbers in the primate lineage, notably in the upper-layer neurons, contributes to increased cognitive abilities. Here, we review major evolutionary changes affecting the apical progenitors in the ventricular zone and focus on the key germinal zone constituting the foundation of neocortical neurogenesis in primates, the outer subventricular zone (OSVZ). We summarize characteristic features of the OSVZ and its key stem cell type, the basal (or outer) radial glia. Next, we concentrate on primate-specific and human-specific genes, expressed in OSVZ-progenitors, the ability of which to amplify these progenitors by targeting the regulation of the cell cycle ultimately underlies the evolutionary increase in upper-layer neurons. Finally, we address likely differences in neocortical development between present-day humans and Neanderthals that are based on human-specific amino acid substitutions in proteins operating in cortical progenitors.
@article{Dehay8683,
author={Colette Dehay, Wieland Huttner},
title={Development and evolution of the primate neocortex from a progenitor cell perspective.},
journal ={Development (Cambridge, England)},
volume={151},
issue ={4},
pages={null--null},
year=2024
}

Robert G. Parton#, Kai Simons#
The Biology of Lipids.
Cold Spring Harb Perspect Biol, Art. No. doi: 10.1101/cshperspect.a041713 (2024)
PubMed Source   

Lipids are the defining features of cellular membranes. They act collectively to form a variety of different structures, and understanding their complex behavior represents an early example of systems biology. A multidisciplinary approach is needed to analyse the functions of lipids in biological systems, and new work is providing fascinating insights into their roles in membrane biology, metabolism, signaling, subcellular dynamics and various disease processes.
@article{Parton8664,
author={Robert G. Parton, Kai Simons},
title={The Biology of Lipids.},
journal ={Cold Spring Harbor perspectives in biology},
volume={},
pages={1--1},
year=2024
}

Dilan Martínez-Torres✳︎, Valentina Maldonado✳︎, Cristian Pérez-Gallardo, Rodrigo Yañez, Valeria Candia, Yannis Kalaidzidis, Marino Zerial, Hernán Morales-Navarrete#, Fabián Segovia-Miranda#
Phenotypic characterization of liver tissue heterogeneity through a next-generation 3D single-cell atlas.
Sci Rep, 14(1) Art. No. 2823 (2024)
Open Access PubMed Source Full Text   

Three-dimensional (3D) geometrical models are potent tools for quantifying complex tissue features and exploring structure-function relationships. However, these models are generally incomplete due to experimental limitations in acquiring multiple (> 4) fluorescent channels in thick tissue sections simultaneously. Indeed, predictive geometrical and functional models of the liver have been restricted to few tissue and cellular components, excluding important cellular populations such as hepatic stellate cells (HSCs) and Kupffer cells (KCs). Here, we combined deep-tissue immunostaining, multiphoton microscopy, deep-learning techniques, and 3D image processing to computationally expand the number of simultaneously reconstructed tissue structures. We then generated a spatial single-cell atlas of hepatic architecture (Hep3D), including all main tissue and cellular components at different stages of post-natal development in mice. We used Hep3D to quantitatively study 1) hepatic morphodynamics from early post-natal development to adulthood, and 2) the effect on the liver's overall structure when changing the hepatic environment after removing KCs. In addition to a complete description of bile canaliculi and sinusoidal network remodeling, our analysis uncovered unexpected spatiotemporal patterns of non-parenchymal cells and hepatocytes differing in size, number of nuclei, and DNA content. Surprisingly, we found that the specific depletion of KCs results in morphological changes in hepatocytes and HSCs. These findings reveal novel characteristics of liver heterogeneity and have important implications for both the structural organization of liver tissue and its function. Our next-gen 3D single-cell atlas is a powerful tool to understand liver tissue architecture, opening up avenues for in-depth investigations into tissue structure across both normal and pathological conditions.
@article{Martínez-Torres8661,
author={Dilan Martínez-Torres, Valentina Maldonado, Cristian Pérez-Gallardo, Rodrigo Yañez, Valeria Candia, Yannis Kalaidzidis, Marino Zerial, Hernán Morales-Navarrete, Fabián Segovia-Miranda},
title={Phenotypic characterization of liver tissue heterogeneity through a next-generation 3D single-cell atlas.},
journal ={Scientific reports},
volume={14},
issue ={1},
pages={null--null},
year=2024
}

Tobias Jumel#, Andrej Shevchenko#
Multispecies Benchmark Analysis for LC-MS/MS Validation and Performance Evaluation in Bottom-Up Proteomics.
J Proteome Res, 23(2) 684-691 (2024)
Open Access PubMed Source   

We present an instrument-independent benchmark procedure and software (LFQ_bout) for the validation and comparative evaluation of the performance of LC-MS/MS and data processing workflows in bottom-up proteomics. The procedure enables a back-to-back comparison of common and emerging workflows, e.g., diaPASEF or ScanningSWATH, and evaluates the impact of arbitrary and inadequately documented settings or black-box data processing algorithms. It enhances the overall performance and quantification accuracy by recognizing and reporting common quantification errors.
@article{Jumel8654,
author={Tobias Jumel, Andrej Shevchenko},
title={Multispecies Benchmark Analysis for LC-MS/MS Validation and Performance Evaluation in Bottom-Up Proteomics.},
journal ={Journal of proteome research},
volume={23},
issue ={2},
pages={684--691},
year=2024
}

Wieland Huttner, Michael Heide, Felipe Mora-Bermúdez, Takashi Namba
Neocortical neurogenesis in development and evolution-Human-specific features.
J Comp Neurol, 532(2) Art. No. e25576 (2024)
Open Access PubMed Source   

In this review, we focus on human-specific features of neocortical neurogenesis in development and evolution. Two distinct topics will be addressed. In the first section, we discuss the expansion of the neocortex during human evolution and concentrate on the human-specific gene ARHGAP11B. We review the ability of ARHGAP11B to amplify basal progenitors and to expand a primate neocortex. We discuss the contribution of ARHGAP11B to neocortex expansion during human evolution and its potential implications for neurodevelopmental disorders and brain tumors. We then review the action of ARHGAP11B in mitochondria as a regulator of basal progenitor metabolism, and how it promotes glutaminolysis and basal progenitor proliferation. Finally, we discuss the increase in cognitive performance due to the ARHGAP11B-induced neocortical expansion. In the second section, we focus on neocortical development in modern humans versus Neanderthals. Specifically, we discuss two recent findings pointing to differences in neocortical neurogenesis between these two hominins that are due to a small number of amino acid substitutions in certain key proteins. One set of such proteins are the kinetochore-associated proteins KIF18a and KNL1, where three modern human-specific amino acid substitutions underlie the prolongation of metaphase during apical progenitor mitosis. This prolongation in turn is associated with an increased fidelity of chromosome segregation to the apical progenitor progeny during modern human neocortical development, with implications for the proper formation of radial units. Another such key protein is transketolase-like 1 (TKTL1), where a single modern human-specific amino acid substitution endows TKTL1 with the ability to amplify basal radial glia, resulting in an increase in upper-layer neuron generation. TKTL1's ability is based on its action in the pentose phosphate pathway, resulting in increased fatty acid synthesis. The data imply greater neurogenesis during neocortical development in modern humans than Neanderthals due to TKTL1, in particular in the developing frontal lobe.
@article{Huttner8642,
author={Wieland Huttner, Michael Heide, Felipe Mora-Bermúdez, Takashi Namba},
title={Neocortical neurogenesis in development and evolution-Human-specific features.},
journal ={The Journal of comparative neurology},
volume={532},
issue ={2},
pages={null--null},
year=2024
}

Fernando Moreto, Jéssica Leite Garcia, Ana Lúcia Dos Anjos Ferreira, Silvia Radrezza, Mariane Róvero Costa, Guilherme Ribeiro Romualdo, Nubia Alves Grandini, Giancarlo Aldini, Camila Renata Correa, Alfonsina D'Amato
Quantitative proteomics study of carnosine effect in an animal model of Western diet-induced nonalcoholic fatty liver disease.
J Biochem Mol Toxicol, 38(2) Art. No. e23644 (2024)
PubMed Source   

The nonalcoholic fatty liver disease (NAFLD), which is closely related to westernized dietary (WD) patterns, displays a rising epidemiological and economic burden. Since there is no pharmacological therapy approved for this disease, mechanistic studies are warranted. In this work, we investigated the action of carnosine (CAR), a natural dipeptide with several protection roles against oxidative stress in the liver of NAFLD rats. NAFLD was induced by WD-rich sugars and fat, verifying the histological evidence of steatosis. As intraperitoneal administration of CAR reversed liver steatosis, the protein profiles of NAFLD liver and CAR NAFLD liver were evaluated by label-free proteomics approach. A total of 2531 proteins were identified and the 230 and 276 were significantly up- and downregulated, respectively, by CAR treatment of NAFLD rats and involved in fundamental pathways such as oxidative stress and lipid metabolism. Perilipin 2 and apolipoprotein E, components of the plasma membrane of vesicle, resulted in highly downregulated in the CAR-treated NAFLD liver. The advanced bioanalytical approach demonstrated the efficacy of CAR in overcoming the main symptoms of NAFLD, ameliorating the steatosis in the liver.
@article{Moreto8678,
author={Fernando Moreto, Jéssica Leite Garcia, Ana Lúcia Dos Anjos Ferreira, Silvia Radrezza, Mariane Róvero Costa, Guilherme Ribeiro Romualdo, Nubia Alves Grandini, Giancarlo Aldini, Camila Renata Correa, Alfonsina D'Amato},
title={Quantitative proteomics study of carnosine effect in an animal model of Western diet-induced nonalcoholic fatty liver disease.},
journal ={Journal of biochemical and molecular toxicology},
volume={38},
issue ={2},
pages={null--null},
year=2024
}

Christopher Schmied#, Michael S Nelson, Sergiy Avilov, Gert-Jan Bakker, Cristina Bertocchi, Johanna Bischof, Ulrike Boehm, Jan Brocher, Mariana T Carvalho, Catalin Chiritescu, Jana Christopher, Beth A Cimini, Eduardo Conde-Sousa, Michael Ebner, Rupert Ecker, Kevin W Eliceiri, Julia Fernandez-Rodriguez, Nathalie Gaudreault, Laurent Gelman, David Grunwald, Tingting Gu, Nadia Halidi, Mathias Hammer, Matthew Hartley, Michael Held, Florian Jug, Varun Kapoor, Ayse Aslihan Koksoy, Judith Lacoste, Sylvia Le Dévédec, Sylvie Le Guyader, Penghuan Liu, Gabriel G Martins, Aastha Mathur, Kyoko Miura, Paula Montero Llopis, Roland Nitschke, Alison J North, Adam C Parslow, Alex Payne-Dwyer, Laure Plantard, Rizwan Ali, Britta Schroth-Diez, Lucas Schütz, Ryan T Scott, Arne Seitz, Olaf Selchow, Ved P Sharma, Martin Spitaler, Sathya Srinivasan, Caterina Strambio-De-Castillia, Dylan J Taatjes, Christian Tischer#, Helena Jambor#
Community-developed checklists for publishing images and image analyses.
Nat Methods, 21(2) 170-181 (2024)
PubMed Source   

Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However, for scientists wishing to publish obtained images and image-analysis results, there are currently no unified guidelines for best practices. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here, we present community-developed checklists for preparing light microscopy images and describing image analyses for publications. These checklists offer authors, readers and publishers key recommendations for image formatting and annotation, color selection, data availability and reporting image-analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby to heighten the quality and explanatory power of microscopy data.
@article{Schmied8645,
author={Christopher Schmied, Michael S Nelson, Sergiy Avilov, Gert-Jan Bakker, Cristina Bertocchi, Johanna Bischof, Ulrike Boehm, Jan Brocher, Mariana T Carvalho, Catalin Chiritescu, Jana Christopher, Beth A Cimini, Eduardo Conde-Sousa, Michael Ebner, Rupert Ecker, Kevin W Eliceiri, Julia Fernandez-Rodriguez, Nathalie Gaudreault, Laurent Gelman, David Grunwald, Tingting Gu, Nadia Halidi, Mathias Hammer, Matthew Hartley, Michael Held, Florian Jug, Varun Kapoor, Ayse Aslihan Koksoy, Judith Lacoste, Sylvia Le Dévédec, Sylvie Le Guyader, Penghuan Liu, Gabriel G Martins, Aastha Mathur, Kyoko Miura, Paula Montero Llopis, Roland Nitschke, Alison J North, Adam C Parslow, Alex Payne-Dwyer, Laure Plantard, Rizwan Ali, Britta Schroth-Diez, Lucas Schütz, Ryan T Scott, Arne Seitz, Olaf Selchow, Ved P Sharma, Martin Spitaler, Sathya Srinivasan, Caterina Strambio-De-Castillia, Dylan J Taatjes, Christian Tischer, Helena Jambor},
title={Community-developed checklists for publishing images and image analyses.},
journal ={Nature methods},
volume={21},
issue ={2},
pages={170--181},
year=2024
}


✳︎ joint first authors, # joint corresponding authors
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