Review
Biotechnology & Applied Microbiology
Paige Allard, Fotini Papazotos, Laurent Potvin-Trottier
Summary: Cells are dynamic, and the development of microfluidic methods allows for tracking and long-term observation of bacterial cells. This review focuses on the recent developments of a microfluidic device known as the mother machine, and discusses the associated analysis methods and modifications to the experimental setup.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Microbiology
Julien Mortier, Stefanie Van Riet, Diana Senovilla Herrero, Kristof Vanoirbeek, Abram Aertsen
Summary: Elucidating phenotypic heterogeneity is important for understanding bacterial behavior and engineering bacteria in biotechnology. This study presents a high-throughput and high-resolution time-lapse fluorescence microscopy-based strategy for screening heterogeneously expressed genes in Bacillus subtilis. The proof-of-concept screening validates this approach.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemical Research Methods
Tao Hu, Shixiong Xu, Lei Wei, Xuegong Zhang, Xiaowo Wang
Summary: Recent advances in long-term time-lapse microscopy have enabled researchers to quantify cell behavior and molecular dynamics with ease. However, the lack of user-friendly software tools optimized for customized research remains a major challenge. CellTracker is a highly integrated graphical user interface software that automates cell segmentation and tracking in time-lapse microscopy images, offering features such as project management, image pre-processing, and statistical analysis.
Article
Biochemical Research Methods
Yanming Zhu, Erik Meijering
Summary: This study proposed a novel NAS-based solution for deep learning-based live cell segmentation in time-lapse microscopy images. By jointly searching non-repeatable micro architectures to construct the macro network and defining a specific search space suitable for the task, as well as exploring temporal information in cell sequences, the method demonstrated more competitive performance, showing more consistent top performance across all datasets in the experiments.
Article
Biochemical Research Methods
Saoirse Amarteifio, Todd Fallesen, Gunnar Pruessner, Giovanni Sena
Summary: This study introduces an algorithm to optimize 3D object tracking by combining registration and tracking tasks into one algorithm, using random sampling to solve the identity management problem. The algorithm is designed and applied in the field of plant biology, and is open-source. It fills a gap in existing tracking techniques by tracking mitotic events in challenging datasets using transient fluorescent markers in unregistered images.
Article
Biotechnology & Applied Microbiology
Xinyang Li, Yixin Li, Yiliang Zhou, Jiamin Wu, Zhifeng Zhao, Jiaqi Fan, Fei Deng, Zhaofa Wu, Guihua Xiao, Jing He, Yuanlong Zhang, Guoxun Zhang, Xiaowan Hu, Xingye Chen, Yi Zhang, Hui Qiao, Hao Xie, Yulong Li, Haoqian Wang, Lu Fang, Qionghai Dai
Summary: DeepCAD-RT is a real-time denoising method for fluorescence time-lapse images, which uses self-supervised deep learning for noise suppression. Compared to traditional methods, DeepCAD-RT significantly reduces the number of network parameters, memory consumption, and processing time, and achieves high imaging signal-to-noise ratio with one-tenth of the photons. In various photon-limited experiments, DeepCAD-RT demonstrates its utility in morphological and functional interrogation of biological dynamics.
NATURE BIOTECHNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Matthias Kist, Domagoj Vucic
Summary: In recent years, research has identified various forms of cell death, each relying on different proteins for activation. Many pathways share components and signaling principles, working together rather than independently. Several cell death regulators are linked to human diseases and may be potential therapeutic targets.
Article
Pharmacology & Pharmacy
Dario Di Giuseppe, Sonia Scarfi, Andrea Alessandrini, Anna Maria Bassi, Serena Mirata, Vanessa Almonti, Gregorio Ragazzini, Andrea Mescola, Monica Filaferro, Rossella Avallone, Giovanni Vitale, Valentina Scognamiglio, Alessandro F. Gualtieri
Summary: This study compared the early cytotoxicity mechanisms of three carcinogenic mineral fibres (chrysotile, crocidolite, and fibrous erionite) using time-lapse video microscopy and in vitro assays. The results showed that fibrous erionite exhibited the earliest toxic effects, while the toxicity of chrysotile and crocidolite increased gradually over time. Chrysotile and crocidolite mainly induced cell death through apoptosis, while erionite exposure may also be associated with a necrotic-like effect.
Article
Biology
Chentao Wen, Takuya Miura, Venkatakaushik Voleti, Kazushi Yamaguchi, Motosuke Tsutsumi, Kei Yamamoto, Kohei Otomo, Yukako Fujie, Takayuki Teramoto, Takeshi Ishihara, Kazuhiro Aoki, Tomomi Nemoto, Elizabeth Mc Hillman, Koutarou D. Kimura
Summary: 3DeeCellTracker is a deep learning-based software pipeline that successfully segments and tracks cells in various dynamic environments, providing a new possibility for revealing cell activities in image datasets that have been difficult to analyze.
Article
Multidisciplinary Sciences
Stathis Hadjidemetriou, Rania Hadjisavva, Andri Christodoulou, Ismini Papageorgiou, Ioanna Panayiotou, Paris Skourides
Summary: This study introduces an automated method for quantifying cell responses, specifically the mitotic cell divisions, over long periods of time using time-lapse video microscopy. The method involves preprocessing, restoration and reconstruction of phase contrast images, and the use of Circle Hough Transform (CHT) for detecting cell centroids and forming spatiotemporal trajectories. The method is validated using experimental video sequences from different cell lines and demonstrates high performance and efficiency.
Article
Multidisciplinary Sciences
Ghazal Azarfar, Ebrahim Aboualizadeh, Simona Ratti, Camilla Olivieri, Alessandra Norici, Michael J. Nasse, Mario Giordano, Carol J. Hirschmugl
Summary: This study utilized mid-infrared spectroscopy to investigate individual Thalassiosira weissflogii cells in water, revealing significant compositional changes in organic pools within the algal cells in response to elevated CO2 concentrations.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Miriam A. Genuth, Yasuhiro Kojima, Doerthe Juelich, Hisanori Kiryu, Scott A. Holley
Summary: Embryonic development involves orderly cell state transitions based on noisy molecular processes. Using single-cell RNA sequencing and in vivo cell tracking data, we defined gene expression and cell motion states. Both states were mapped onto embryos and the dynamics of state transitions were studied using cell motion states. The reproducible pattern of cell motion states and bilateral symmetry arise from temporal averaging, while individual embryos exhibit transient deviations forming left-right asymmetries in collective cell motion. Collective cell behavior can be a source of asymmetry rather than a buffer against noisy individual cell behavior.
Article
Multidisciplinary Sciences
Maddalena Nano, James A. Mondo, Jacob Harwood, Varuzhan Balasanyan, Denise J. Montell
Summary: Executioner-caspase activation has long been considered irreversible in apoptosis. However, studies have shown that cells can survive caspase activation induced by drugs or radiation. This study aimed to investigate whether cells can recover from direct caspase activation without drug-induced pro-survival stress responses. The results revealed that cells can indeed survive direct caspase activation, and heterogeneities in cellular state can modify the outcome of potentially lethal caspase activity, which may explain incomplete tumor cell killing in response to apoptosis-inducing cancer treatments.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biology
Guillaume Ravel, Michel Bergmann, Alain Trubuil, Julien Deschamps, Romain Briandet, Simon Labarthe
Summary: Biofilms are organized communities of microorganisms with increased tolerance to antimicrobials. Swimmer bacilli in pathogenic biofilms can counterbalance this tolerance by delivering antimicrobial agents or creating a vascularization network. A new methodology was developed to analyze swimmer trajectories in biofilm matrix, providing insights into the mechanisms of adaptation and optimizing biocontrol strategies.
Article
Engineering, Mechanical
M. A. Bashar Emon, Samantha Knoll, Umnia Doha, Lauren Ladehoff, Luke Lalonde, Danielle Baietto, Mayandi Sivaguru, Rohit Bhargava, M. Taher A. Saif
Summary: It has been shown that cells exhibit different contractile responses to light of different wavelengths and intensities, with lower light intensities below specific thresholds not perturbing cell force homeostasis. Cell traction is highly sensitive to the effect of light on cells, and lower than previously reported safe thresholds are dose-independent, suggesting a highly sensitive readout of cell response to light.
EXTREME MECHANICS LETTERS
(2021)
Article
Biotechnology & Applied Microbiology
Tereza Fabryova, David Kubac, Marek Kuzma, Pavel Hrouzek, Jiri Kopecky, Lenka Tumova, Jose Cheel
Summary: This study isolated lutein from a chlorophyll-deficient Parachlorella kessleri HY1 strain using high-performance countercurrent chromatography (HPCCC), improving production efficiency and recovery rate with a multiple injection method. The results provide an efficient and economical basis for large-scale production of microalgae-sourced lutein.
JOURNAL OF APPLIED PHYCOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Tomas Grivalsky, Antonin Strizek, Pavel Pribyl, Jaromir Lukavsky, Radim Cegan, Roman Hobza, Pavel Hrouzek
Summary: Detection of fast-growing green algae Chlorella vulgaris as a contaminant in diatom Phaeodactylum tricornutum cultures using various approaches reveals PCR/qPCR as the most reliable and sensitive method with a detection sensitivity close to 75 cells/mL. This method is effective even in mixed cultures containing a large number of P. tricornutum cells. The cultivation media exchange method from sea water to fresh water is similarly sensitive to PCR approaches for detecting contaminants, albeit with a longer detection time.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Chemistry, Medicinal
Daniela Barcenas-Perez, Antonin Strizek, Pavel Hrouzek, Jiri Kopecky, Marta Barradas, Arantzazu Sierra-Ramirez, Pablo J. Fernandez-Marcos, Jose Cheel
Summary: This study developed a multiple sequential injection HPCCC method to isolate fucoxanthin from Phaeodactylum tricornutum with high purity and recovery. The isolated fucoxanthin retained its biological activity and may provide a useful model for producing fucoxanthin from diatom biomass. Environmental risk and general process evaluation factors were used to assess the developed separation method and compare it with existing methods.
Article
Plant Sciences
David P. Fewer, Jouni Jokela, Lassi Heinila, Reidun Aesoy, Kaarina Sivonen, Tomas Galica, Pavel Hrouzek, Lars Herfindal
Summary: Cyanobacteria produce diverse cyclic lipopeptides with potent antifungal activities, targeting a range of human and plant fungal pathogens. These lipopeptides act through membrane disruption and exhibit cytotoxicity in human cells. Their complex biosynthetic pathways promote chemical diversity, but their origins and mechanisms of structural diversification remain poorly understood. The production of these lipopeptides benefits the producer, either through their antifungal activity or other physiological functions, highlighting their potential biotechnological and therapeutic applications.
PHYSIOLOGIA PLANTARUM
(2021)
Article
Multidisciplinary Sciences
Marek Kuzma, Jan Hajek, Pavel Hrouzek, Alastair T. Gardiner, Martin Lukes, Martin Moos, Petr Simek, Michal Koblizek, Nupur
Summary: Gemmatimonas phototrophica AP64 is the first phototrophic representative of the bacterial phylum Gemmatimonadetes. The carotenoid gemmatoxanthin extracted from its cells contains 11 conjugated double bonds and methoxy, carboxyl, and aldehyde groups. This is the first report of a linear C40 carotenoid backbone with carboxyl, methoxy, and aldehyde groups.
SCIENTIFIC REPORTS
(2021)
Article
Biotechnology & Applied Microbiology
Dominika Cincarova, Jan Hajek, Martin Dobrichovsky, Martin Lukes, Pavel Hrouzek
Summary: This study found that the quantification of pheophorbide a using the USP-NFP method significantly exceeded that of the HPLC-HRMS method, mainly due to the integration of all pheophorbide variants by USP-NFP. The suitable extraction solvent for pheophorbide a was determined to be 60% acetone, however, the extraction process might generate high activity of chlorophyllase. Inactivation of chlorophyllase through high-temperature treatment was effective in ensuring the stability and accurate quantification of pheophorbide a.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2021)
Article
Microbiology
Subhasish Saha, Paul-Adrian Bulzu, Petra Urajova, Jan Mares, Grzegorz Konert, Joao Camara Manoel, Marketa Macho, Daniela Ewe, Pavel Hrouzek, Jiri Masojidek, Rohit Ghai, Kumar Saurav
Summary: The regulation of cyanopeptide production is crucial for understanding their ecological role, and our study sheds light on the control of microviridin production by epibionts through quorum-sensing mechanisms, suggesting their widespread presence in natural cyanobacterial bloom community regulation.
Article
Biochemistry & Molecular Biology
Katerina Delawska, Petra Divoka, David Sedlak, Marek Kuzma, Kumar Saurav, Marketa Macho, Gabor Steinbach, Pavel Hrouzek
Summary: Scytophycins, such as tolytoxin, are actin disrupting macrolides with potent antiproliferative effects on human cells. Structurally different analogues like 7-O-methylscytophycin B exhibit varying levels of cytotoxicity. These compounds increase caspases 3/7 levels in cells but show no activity in cells lacking specific proteins, indicating a mitochondria-dependent apoptosis pathway. Further research on structure-activity relationships in scytophycins is encouraged for potential targeted drug delivery applications.
Article
Entomology
Silvie Dostalkova, Petra Urajova, Dominika Cincarova, Tereza Vranova, Pavel Hrouzek, Marek Petrivalsky, Martin Lukes, Radmila Capkova Frydrychova, Jiri Danihlik
Summary: Extracts from Chlorella vulgaris demonstrated significant antimicrobial activity against Paenibacillus larvae, the causative agent of American foulbrood in honey bees, particularly targeting different genotypes. The active fractions contained specific chemical components, suggesting potential prophylactic properties for honey bee health in Chlorella food supplements.
JOURNAL OF APICULTURAL RESEARCH
(2021)
Article
Multidisciplinary Sciences
Pu Qian, Alastair T. Gardiner, Ivana Simova, Katerina Naydenova, Tristan Croll, Philip J. Jackson, Nupur, Miroslav Kloz, Petra Cubakova, Marek Kuzma, Yonghui Zeng, Pablo Castro-Hartmann, Bart van Knippenberg, Kenneth N. Goldie, David Kaftan, Pavel Hrouzek, Jan Hajek, Jon Agirre, C. Alistair Siebert, David Bina, Kasim Sader, Henning Stahlberg, Roman Sobotka, Christopher J. Russo, Tomas Polivka, C. Neil Hunter, Michal Koblizek
Summary: Phototrophic Gemmatimonadetes have evolved the ability to use solar energy through horizontal gene transfer. The study reveals the unique solar energy harvesting and trapping architecture of Gemmatimonas phototrophica, as well as the flow of energy within the complex.
Article
Chemistry, Multidisciplinary
Kumar Saurav, Alessia Caso, Petra Urajova, Pavel Hrouzek, Germana Esposito, Katerina Delawska, Marketa Macho, Jan Hajek, Jose Cheel, Subhasish Saha, Petra Divoka, Sila Arsin, Kaarina Sivonen, David P. Fewer, Valeria Costantino
Summary: PUW and MIN are structurally homologous cyclic lipopeptides with antifungal and cytotoxic activities, where the variation in fatty acid substitutions influences the cytotoxicity of the compounds. Different substitutions on the fatty acid moiety of PUW/MIN variants lead to varying degrees of cytotoxicity. A 63 kb puwainaphycin biosynthetic gene cluster was identified in the N. harveyana strain UHCC-0300, indicating the presence of specific lipoinitiation mechanisms and enzymes for modifying the fatty acid moiety.
Article
Biotechnology & Applied Microbiology
Daniela Barcenas-Perez, Martin Lukes, Pavel Hrouzek, Jakub Zapal, Marek Kuzma, Jiri Kopecky, David Kubac, Bertha O. Arredondo-Vega, Jose Cheel
Summary: In this study, pure EPA ethyl ester was efficiently produced from Nanofrustulum shiloi biomass using high performance countercurrent chromatography. The process achieved high purity and recovery of the EPA fraction, making it a useful model for the efficient production of pure EPA from microalgae.
JOURNAL OF APPLIED PHYCOLOGY
(2022)
Article
Chemistry, Organic
L. M. P. Heinila, J. Jokela, M. N. Ahmed, M. Wahlsten, S. Kumar, P. Hrouzek, P. Permi, H. Koistinen, D. P. Fewer, K. Sivonen
Summary: This study reports the discovery of novel natural products called varlaxins, members of the aeruginosin family. The chemical structures of varlaxins 1046A and 1022A were determined, and they were found to strongly inhibit human serine proteases.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Jan Hajek, Sebastian Bieringer, Katerina Voracova, Marketa Macho, Kumar Saurav, Katerina Delawska, Petra Divoka, Radovan Fiser, Gabriela Mikusova, Jose Cheel, David P. Fewer, Dai Long Vu, Jindriska Paichlova, Herbert Riepl, Pavel Hrouzek
Summary: Microbial cyclic lipopeptides have potential as antifungal agents, but their cytotoxicity hinders their application. This study demonstrated that varying fatty acid chain lengths in PUWs/MINs cyclic lipopeptides impact their cytotoxicity and antifungal efficacy. Modifying the fatty acid tails can enhance antifungal activity while reducing cytotoxicity, suggesting the development of semi-synthetic lipopeptide variants with improved and selective antifungal activities.
Article
Microbiology
Subhasish Saha, Nabila Mohammad Ishaque, Ilia Burgsdorf, Marketa Macho, Daniela Ewe, Laura Steindler, Pavel Hrouzek, Krishnan Kannabiran, Kumar Saurav
Summary: This study presents the draft genome sequence of Streptomyces sp. strain VITNK9 isolated from a soil sample collected in Vellore District, Tamil Nadu, India, with an assembly size of 7,920,076 bp and 72.7% GC content.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
