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  • 1
    Publication Date: 2024-04-22
    Description: Ocean color remote sensing has been used for more than 2 decades to estimate primary productivity. Approaches have also been developed to disentangle phytoplankton community structure based on spectral data from space, in particular when combined with in situ measurements of photosynthetic pigments. Here, we propose a new ocean color algorithm to derive the relative cell abundance of seven phytoplankton groups, as well as their contribution to total chlorophyll a (Chl a ) at the global scale. Our algorithm is based on machine learning and has been trained using remotely sensed parameters (reflectance, backscattering, and attenuation coefficients at different wavelengths, plus temperature and Chl a ) combined with an omics-based biomarker developed using Tara Oceans data representing a single-copy gene encoding a component of the photosynthetic machinery that is present across all phytoplankton, including both prokaryotes and eukaryotes. It differs from previous methods which rely on diagnostic pigments to derive phytoplankton groups. Our methodology provides robust estimates of the phytoplankton community structure in terms of relative cell abundance and contribution to total Chl a concentration. The newly generated datasets yield complementary information about different aspects of phytoplankton that are valuable for assessing the contributions of different phytoplankton groups to primary productivity and inferring community assembly processes. This makes remote sensing observations excellent tools to collect essential biodiversity variables (EBVs) and provide a foundation for developing marine biodiversity forecasts.
    Keywords: Cell Biology ; Developmental Biology ; Embryology ; Anatomy ; SELF-ORGANIZING MAPS ; OCEAN COLOR ; MARINE-PHYTOPLANKTON ; MEDITERRANEAN ; SEALIGHT-ABSORPTION ; BIODIVERSITY ; PIGMENTS
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 2
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    Springer Nature
    Publication Date: 2024-04-06
    Description: Developmental Biology; Plant Sciences; Cell Biology
    Keywords: Developmental Biology ; Plant Sciences ; Cell Biology ; thema EDItEUR::K Economics, Finance, Business and Management::KN Industry and industrial studies::KND Manufacturing industries ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences ; thema EDItEUR::T Technology, Engineering, Agriculture, Industrial processes::TC Biochemical engineering
    Language: English
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  • 3
    Publication Date: 2024-04-05
    Description: The charophytes are the group of green algae that are anestral and most closely related to land plants. Today, these organisms are not only important in evoutionary studies but have become outstanding model organisms for plant research.
    Keywords: QK1-989 ; Q1-390 ; Charophytes ; Micrasterias ; plant ; evolution ; Model organisms ; Chara ; Penium ; Cell Biology ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PST Botany and plant sciences
    Language: English
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  • 4
    Publication Date: 2024-04-05
    Description: This open access textbook leads the reader from basic concepts of chromatin structure and function and RNA mechanisms to the understanding of epigenetics, imprinting, regeneration and reprogramming. The textbook treats epigenetic phenomena in animals, as well as plants. Written by four internationally known experts and senior lecturers in this field, it provides a valuable tool for Master- and PhD- students who need to comprehend the principles of epigenetics, or wish to gain a deeper knowledge in this field. After reading this book, the student will: Have an understanding of the basic toolbox of epigenetic regulation Know how genetic and epigenetic information layers are interconnected Be able to explain complex epigenetic phenomena by understanding the structures and principles of the underlying molecular mechanisms Understand how misregulated epigenetic mechanisms can lead to disease
    Keywords: Genetics and Genomics ; Biomedicine, general ; Cell Biology ; Human Genetics ; Epigenetics ; Biomedical Research ; Medical Genetics ; Cancer ; Chromatin ; Chromatin Dynamics ; Cellular Memory ; DNA Methylation ; Epigenetic Textbook ; Gene Regulation ; Gene Silencing ; Histone Modification ; Imprinting ; Inheritance ; Metabolism ; Nucleus ; Open Access ; Pluripotency ; Reprogramming ; RNA Mechanisms ; Transcription ; X Chromosome inactivation ; Genetics (non-medical) ; Medical research ; Cellular biology (cytology) ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAK Genetics (non-medical) ; thema EDItEUR::M Medicine and Nursing::MB Medicine: general issues::MBG Medical equipment and techniques ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSB Biochemistry ; thema EDItEUR::M Medicine and Nursing::MF Pre-clinical medicine: basic sciences::MFN Medical genetics
    Language: English
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  • 5
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    Springer Nature
    Publication Date: 2024-03-30
    Description: Pharmacology/Toxicology; Molecular Medicine; Human Physiology; Immunology; Cell Biology
    Keywords: Pharmacology/Toxicology ; Molecular Medicine ; Human Physiology ; Immunology ; Cell Biology ; thema EDItEUR::K Economics, Finance, Business and Management::KJ Business and Management::KJM Management and management techniques::KJMV Management of specific areas ; thema EDItEUR::K Economics, Finance, Business and Management::KN Industry and industrial studies::KNB Energy industries and utilities ; thema EDItEUR::K Economics, Finance, Business and Management::KN Industry and industrial studies::KND Manufacturing industries ; thema EDItEUR::M Medicine and Nursing ; thema EDItEUR::T Technology, Engineering, Agriculture, Industrial processes::TC Biochemical engineering
    Language: English
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  • 6
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    Springer Nature
    Publication Date: 2023-03-03
    Description: Human Physiology, Endocrinology, Cell Biology, Neurosciences
    Keywords: Human Physiology ; Endocrinology ; Cell Biology ; Neurosciences ; bic Book Industry Communication::M Medicine::MB Medicine: general issues::MBD Medical profession
    Language: English
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  • 7
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hirst, W. G., Kiefer, C., Abdosamadi, M. K., Schäffer, E., & Reber, S. In Vitro reconstitution and imaging of microtubule dynamics by fluorescence and label-free microscopy. STAR Protocols, 1(3), (2020): 100177, doi:10.1016/j.xpro.2020.100177.
    Description: Dynamic microtubules are essential for many processes in the lives of eukaryotic cells. To study and understand the mechanisms of microtubule dynamics and regulation, in vitro reconstitution with purified components has proven a vital approach. Imaging microtubule dynamics can be instructive for a given species, isoform composition, or biochemical modification. Here, we describe two methods that visualize microtubule dynamics at high speed and high contrast: (1) total internal reflection fluorescence microscopy and (2) label-free interference reflection microscopy.
    Description: We thank the AMBIO imaging facility (Charité, Berlin) and Nikon at MBL for imaging support. We thank all former and current members of the Reber lab for discussion and helpful advice, in particular Christoph Hentschel and Soma Zsoter for technical assistance. S.R. acknowledges funding by the IRI Life Sciences (Humboldt-Universität zu Berlin, Excellence Initiative/DFG). W.H. was supported by the Alliance Berlin Canberra co-funded by a grant from the Deutsche Forschungsgemeinschaft (DFG) for the International Research Training Group (IRTG) 2290 and the Australian National University. C.K. thanks the Deutsche Forschungsgesellschaft (DFG, JA 2589/1-1). C.K. and M.A. thank Steve Simmert and Tobias Jachowski former and current members of the Schäffer lab.
    Keywords: Biophysics ; Cell Biology ; Microscopy
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 8
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Geisterfer, Z. M., Oakey, J., & Gatlin, J. C. . Microfluidic encapsulation of Xenopus laevis cell-free extracts using hydrogel photolithography. STAR Protocols, 1(3), (2020): 100221, doi:10.1016/j.xpro.2020.100221.
    Description: Cell-free extract derived from the eggs of the African clawed frog Xenopus laevis is a well-established model system that has been used historically in bulk aliquots. Here, we describe a microfluidic approach for isolating discrete, biologically relevant volumes of cell-free extract, with more expansive and precise control of extract shape compared with extract-oil emulsions. This approach is useful for investigating the mechanics of intracellular processes affected by cell geometry or cytoplasmic volume, including organelle scaling and positioning mechanisms. For complete details on the use and execution of this protocol, please refer to Geisterfer et al. (2020).
    Description: This work was made possible by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant no. 2P20GM103432. It was also supported by additional funding provided by the NIGMS under grant no. R01GM113028, the NSF Faculty CAREER Program under award no. BBBE 1254608, Whitman Center fellowships at the Marine Biological Laboratory, and the Biomedical Scholars program of the Pew Charitable Trusts. We thank Drs. Aaron Groen and Tim Mitchison for their intellectual contributions and involvement in some of the pioneering experiments that set the foundation for this approach.
    Keywords: Biophysics ; Cell Biology ; Cell isolation ; Microscopy ; Model Organisms
    Repository Name: Woods Hole Open Access Server
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  • 9
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    American Association for the Advancement of Science (AAAS)
    In: Science
    Publication Date: 2018-12-21
    Keywords: Cell Biology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2018-12-21
    Description: The endosomal sorting complexes required for transport (ESCRTs) catalyze reverse-topology scission from the inner face of membrane necks in HIV budding, multivesicular endosome biogenesis, cytokinesis, and other pathways. We encapsulated ESCRT-III subunits Snf7, Vps24, and Vps2 and the AAA+ ATPase (adenosine triphosphatase) Vps4 in giant vesicles from which membrane nanotubes reflecting the correct topology of scission could be pulled. Upon ATP release by photo-uncaging, this system generated forces within the nanotubes that led to membrane scission in a manner dependent upon Vps4 catalytic activity and Vps4 coupling to the ESCRT-III proteins. Imaging of scission revealed Snf7 and Vps4 puncta within nanotubes whose presence followed ATP release, correlated with force generation and nanotube constriction, and preceded scission. These observations directly verify long-standing predictions that ATP-hydrolyzing assemblies of ESCRT-III and Vps4 sever membranes.
    Keywords: Cell Biology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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