| 1. |
- Babbitt, Patricia C., et al.
(author)
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Creating a specialist protein resource network : a meeting report for the protein bioinformatics and community resources retreat
- 2015
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In: Database. - : Oxford University Press (OUP). - 1758-0463.
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Journal article (peer-reviewed)abstract
- During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.
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| 2. |
- Kim, Anna A, et al.
(author)
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Microfluidics for mechanobiology of model organisms
- 2018
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In: Microfluidics in Cell Biology Part A. - : Elsevier. - 9780128142806 ; , s. 217-259
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Book chapter (peer-reviewed)abstract
- Mechanical stimuli play a critical role in organ development, tissue homeostasis, and disease. Understanding how mechanical signals are processed in multicellular model systems is critical for connecting cellular processes to tissue- and organism-level responses. However, progress in the field that studies these phenomena, mechanobiology, has been limited by lack of appropriate experimental techniques for applying repeatable mechanical stimuli to intact organs and model organisms. Microfluidic platforms, a subgroup of microsystems that use liquid flow for manipulation of objects, are a promising tool for studying mechanobiology of small model organisms due to their size scale and ease of customization. In this work, we describe design considerations involved in developing a microfluidic device for studying mechanobiology. Then, focusing on worms, fruit flies, and zebrafish, we review current microfluidic platforms for mechanobiology of multicellular model organisms and their tissues and highlight research opportunities in this developing field.
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| 3. |
- Kim, Anna A, et al.
(author)
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Regional Calcium Dynamics in Drosophila Adult Midgut
- 2019
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In: Mol. Biol. Cell.
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Conference paper (other academic/artistic)abstract
- Although calcium dynamics are widely studied in cell culture, little has been reported on the topic for adult organs. We find striking regional and cell-type specific differences in calcium dynamics in the three major cell types of the adult Drosophila intestine. The adult fruit fly intestine is a compelling platform for studying intercellular dynamics and interactions. This stem cell-based epithelium is a reductionist model system of the mammalian small bowel with conserved features. The multi-cellular epithelium consists of three major cell types: progenitor cells that give rise to new cells (including stem cells), enteroendocrine cells that are hormone signaling cells, and enterocytes that are large absorptive cells.We find regional and cell-type specific variations in calcium signaling dynamics within this functionally compartmentalized organ, using confocal imaging of ex vivo cultured fly intestines. Progenitor and enteroendocrine cells indicate oscillatory intracellular calcium dynamics of slower and faster frequencies respectively, and enterocytes demonstrate the presence of traveling calcium waves. Our findings may establish a novel model for studying spatio-temporal organization of cellular to organ-level calcium dynamics in a renewable adult organ.
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| 4. |
- Nekimken, A. L., et al.
(author)
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Pneumatic stimulation of C. elegans mechanoreceptor neurons in a microfluidic trap
- 2017
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In: Lab on a Chip - Miniaturisation for Chemistry and Biology. - : Royal Society of Chemistry (RSC). - 1473-0189 .- 1473-0197. ; 17:6, s. 1116-1127
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Journal article (peer-reviewed)abstract
- New tools for applying force to animals, tissues, and cells are critically needed in order to advance the field of mechanobiology, as few existing tools enable simultaneous imaging of tissue and cell deformation as well as cellular activity in live animals. Here, we introduce a novel microfluidic device that enables high-resolution optical imaging of cellular deformations and activity while applying precise mechanical stimuli to the surface of the worm's cuticle with a pneumatic pressure reservoir. To evaluate device performance, we compared analytical and numerical simulations conducted during the design process to empirical measurements made with fabricated devices. Leveraging the well-characterized touch receptor neurons (TRNs) with an optogenetic calcium indicator as a model mechanoreceptor neuron, we established that individual neurons can be stimulated and that the device can effectively deliver steps as well as more complex stimulus patterns. This microfluidic device is therefore a valuable platform for investigating the mechanobiology of living animals and their mechanosensitive neurons.
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