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Balachandra S, Amodeo AA. Bellymount-Pulsed Tracking: A Novel Approach for Real-Time In vivo Imaging of Drosophila Abdominal Tissues. bioRxiv 2024:2024.03.31.587498. [PMID: 38617254 PMCID: PMC11014545 DOI: 10.1101/2024.03.31.587498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Quantitative live imaging is a valuable tool that offers insights into cellular dynamics. However, many fundamental biological processes are incompatible with current live imaging modalities. Drosophila oogenesis is a well-studied system that has provided molecular insights into a range of cellular and developmental processes. The length of the oogenesis coupled with the requirement for inputs from multiple tissues has made long-term culture challenging. Here, we have developed Bellymount-Pulsed Tracking (Bellymount-PT), which allows continuous, non-invasive live imaging of Drosophila oogenesis inside the female abdomen for up to 16 hours. Bellymount-PT improves upon the existing Bellymount technique by adding pulsed anesthesia with periods of feeding that support the long-term survival of flies during imaging. Using Bellymount-PT we measure key events of oogenesis including egg chamber growth, yolk uptake, and transfer of specific proteins to the oocyte during nurse cell dumping with high spatiotemporal precision within the abdomen of a live female.
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Affiliation(s)
- Shruthi Balachandra
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Amanda A Amodeo
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
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2
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Giri A, Kar S. Interlinked bi-stable switches govern the cell fate commitment of embryonic stem cells. FEBS Lett 2024; 598:915-934. [PMID: 38408774 DOI: 10.1002/1873-3468.14832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/23/2023] [Accepted: 02/03/2024] [Indexed: 02/28/2024]
Abstract
The development of embryonic stem (ES) cells to extraembryonic trophectoderm and primitive endoderm lineages manifests distinct steady-state expression patterns of two key transcription factors-Oct4 and Nanog. How dynamically such kind of steady-state expressions are maintained remains elusive. Herein, we demonstrate that steady-state dynamics involving two bistable switches which are interlinked via a stepwise (Oct4) and a mushroom-like (Nanog) manner orchestrate the fate specification of ES cells. Our hypothesis qualitatively reconciles various experimental observations and elucidates how different feedback and feedforward motifs orchestrate the extraembryonic development and stemness maintenance of ES cells. Importantly, the model predicts strategies to optimize the dynamics of self-renewal and differentiation of embryonic stem cells that may have therapeutic relevance in the future.
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Affiliation(s)
- Amitava Giri
- Department of Chemistry, IIT Bombay, Powai, India
| | - Sandip Kar
- Department of Chemistry, IIT Bombay, Powai, India
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3
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Coomer MA, Ham L, Stumpf MPH. Noise distorts the epigenetic landscape and shapes cell-fate decisions. Cell Syst 2021:S2405-4712(21)00339-2. [PMID: 34626539 DOI: 10.1016/j.cels.2021.09.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 06/21/2021] [Accepted: 09/02/2021] [Indexed: 12/24/2022]
Abstract
The Waddington epigenetic landscape has become an iconic representation of the cellular differentiation process. Recent single-cell transcriptomic data provide new opportunities for quantifying this originally conceptual tool, offering insight into the gene regulatory networks underlying cellular development. While many methods for constructing the landscape have been proposed, by far the most commonly employed approach is based on computing the landscape as the negative logarithm of the steady-state probability distribution. Here, we use simple models to highlight the complexities and limitations that arise when reconstructing the potential landscape in the presence of stochastic fluctuations. We consider how the landscape changes in accordance with different stochastic systems and show that it is the subtle interplay between the deterministic and stochastic components of the system that ultimately shapes the landscape. We further discuss how the presence of noise has important implications for the identifiability of the regulatory dynamics from experimental data. A record of this paper's transparent peer review process is included in the supplemental information.
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Xu Y, Zhang J, Hu Y, Li X, Sun L, Peng Y, Sun Y, Liu B, Bian Z, Rong Z. Single-cell transcriptome analysis reveals the dynamics of human immune cells during early fetal skin development. Cell Rep 2021; 36:109524. [PMID: 34380039 DOI: 10.1016/j.celrep.2021.109524] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 05/12/2021] [Accepted: 07/22/2021] [Indexed: 01/12/2023] Open
Abstract
The immune system of skin develops in stages in mice. However, the developmental dynamics of immune cells in human skin remains elusive. Here, we perform transcriptome profiling of CD45+ hematopoietic cells in human fetal skin at an estimated gestational age of 10-17 weeks by single-cell RNA sequencing. A total of 13 immune cell types are identified. Skin macrophages show dynamic heterogeneity over the course of skin development. A major shift in lymphoid cell developmental states occurs from the first to the second trimester that implies an in situ differentiation process. Gene expression analysis reveals a typical developmental program in immune cells in accordance with their functional maturation, possibly involving metabolic reprogramming. Finally, we identify transcription factors (TFs) that potentially regulate cellular transitions by comparing TFs and TF target gene networks. These findings provide detailed insight into how the immune system of the human skin is established during development.
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Affiliation(s)
- Yingping Xu
- Experimental Research Center, Dermatology Hospital, Southern Medical University, Guangzhou 510091, China.
| | - Jun Zhang
- Experimental Research Center, Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Yongfei Hu
- Experimental Research Center, Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Xuefei Li
- Experimental Research Center, Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Lihua Sun
- Development of Gynaecology and Obstetrics, Nanhai Hospital, Southern Medical University, Guangzhou 528200, China
| | - Yu Peng
- Experimental Research Center, Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Yuzhe Sun
- Experimental Research Center, Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Bing Liu
- State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Zhilei Bian
- Department of Hematology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450052, China.
| | - Zhili Rong
- Experimental Research Center, Dermatology Hospital, Southern Medical University, Guangzhou 510091, China; Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China.
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5
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Baran-Gale J, Morgan MD, Maio S, Dhalla F, Calvo-Asensio I, Deadman ME, Handel AE, Maynard A, Chen S, Green F, Sit RV, Neff NF, Darmanis S, Tan W, May AP, Marioni JC, Ponting CP, Holländer GA. Ageing compromises mouse thymus function and remodels epithelial cell differentiation. eLife 2020; 9:e56221. [PMID: 32840480 PMCID: PMC7490013 DOI: 10.7554/elife.56221] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 08/22/2020] [Indexed: 12/13/2022] Open
Abstract
Ageing is characterised by cellular senescence, leading to imbalanced tissue maintenance, cell death and compromised organ function. This is first observed in the thymus, the primary lymphoid organ that generates and selects T cells. However, the molecular and cellular mechanisms underpinning these ageing processes remain unclear. Here, we show that mouse ageing leads to less efficient T cell selection, decreased self-antigen representation and increased T cell receptor repertoire diversity. Using a combination of single-cell RNA-seq and lineage-tracing, we find that progenitor cells are the principal targets of ageing, whereas the function of individual mature thymic epithelial cells is compromised only modestly. Specifically, an early-life precursor cell population, retained in the mouse cortex postnatally, is virtually extinguished at puberty. Concomitantly, a medullary precursor cell quiesces, thereby impairing maintenance of the medullary epithelium. Thus, ageing disrupts thymic progenitor differentiation and impairs the core immunological functions of the thymus.
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Affiliation(s)
| | - Michael D Morgan
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Cancer Research United Kingdom - Cambridge Institute, Li Ka Shing Centre, University of CambridgeCambridgeUnited Kingdom
| | - Stefano Maio
- Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
- Department of Paediatrics, University of Oxford, Cancer ResearchOxfordUnited Kingdom
| | - Fatima Dhalla
- Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
- Department of Paediatrics, University of Oxford, Cancer ResearchOxfordUnited Kingdom
| | - Irene Calvo-Asensio
- Department of Biomedicine, University of Basel, and University Children’s HospitalBaselSwitzerland
| | - Mary E Deadman
- Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
- Department of Paediatrics, University of Oxford, Cancer ResearchOxfordUnited Kingdom
| | - Adam E Handel
- Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
| | | | - Steven Chen
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Foad Green
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Rene V Sit
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Norma F Neff
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | | | - Weilun Tan
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Andy P May
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - John C Marioni
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Cancer Research United Kingdom - Cambridge Institute, Li Ka Shing Centre, University of CambridgeCambridgeUnited Kingdom
- EMBL-EBI, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Chris P Ponting
- MRC Human Genetics Unit, University of EdinburghEdinburghUnited Kingdom
| | - Georg A Holländer
- Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
- Department of Paediatrics, University of Oxford, Cancer ResearchOxfordUnited Kingdom
- Department of Biomedicine, University of Basel, and University Children’s HospitalBaselSwitzerland
- Department of Biosystems Science and Engineering, ETH ZurichBaselSwitzerland
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Li J, Han S, Li H, Udeshi ND, Svinkina T, Mani DR, Xu C, Guajardo R, Xie Q, Li T, Luginbuhl DJ, Wu B, McLaughlin CN, Xie A, Kaewsapsak P, Quake SR, Carr SA, Ting AY, Luo L. Cell-Surface Proteomic Profiling in the Fly Brain Uncovers Wiring Regulators. Cell 2020; 180:373-386.e15. [PMID: 31955847 DOI: 10.1016/j.cell.2019.12.029] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 01/12/2023]
Abstract
Molecular interactions at the cellular interface mediate organized assembly of single cells into tissues and, thus, govern the development and physiology of multicellular organisms. Here, we developed a cell-type-specific, spatiotemporally resolved approach to profile cell-surface proteomes in intact tissues. Quantitative profiling of cell-surface proteomes of Drosophila olfactory projection neurons (PNs) in pupae and adults revealed global downregulation of wiring molecules and upregulation of synaptic molecules in the transition from developing to mature PNs. A proteome-instructed in vivo screen identified 20 cell-surface molecules regulating neural circuit assembly, many of which belong to evolutionarily conserved protein families not previously linked to neural development. Genetic analysis further revealed that the lipoprotein receptor LRP1 cell-autonomously controls PN dendrite targeting, contributing to the formation of a precise olfactory map. These findings highlight the power of temporally resolved in situ cell-surface proteomic profiling in discovering regulators of brain wiring.
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Affiliation(s)
- Jiefu Li
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| | - Shuo Han
- Departments of Genetics, Biology, and Chemistry, Chan Zuckerberg Biohub, Stanford University, Stanford, CA 94305, USA
| | - Hongjie Li
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Namrata D Udeshi
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tanya Svinkina
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - D R Mani
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chuanyun Xu
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Ricardo Guajardo
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Qijing Xie
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Tongchao Li
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - David J Luginbuhl
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Bing Wu
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Colleen N McLaughlin
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Anthony Xie
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Pornchai Kaewsapsak
- Departments of Genetics, Biology, and Chemistry, Chan Zuckerberg Biohub, Stanford University, Stanford, CA 94305, USA
| | - Stephen R Quake
- Departments of Bioengineering and Applied Physics, Chan Zuckerberg Biohub, Stanford University, Stanford, CA 94305, USA
| | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alice Y Ting
- Departments of Genetics, Biology, and Chemistry, Chan Zuckerberg Biohub, Stanford University, Stanford, CA 94305, USA.
| | - Liqun Luo
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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Yang F, Gong XY, Liu HT, Schäufele R, Schnyder H. Effects of nitrogen and vapour pressure deficit on phytomer growth and development in a C4 grass. AoB Plants 2017; 8:plw075. [PMID: 27810947 PMCID: PMC5206350 DOI: 10.1093/aobpla/plw075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 10/19/2016] [Indexed: 05/12/2023]
Abstract
Phytomers are basic morphological units of plants. Knowledge of phytomer development is essential for understanding morphological plasticity, functional-structural modelling of plant growth and the usage of leaf characteristics to indicate growth conditions at the time of production (e.g. stable isotope signals). Yet, systematic analysis on the process of phytomer development is unavailable for wild or perennial C4 grasses. Also, effects of environmental factors, such as nitrogen nutrition or vapour pressure deficit (VPD), on coordination events of developmental processes of C4 grasses have not been studied. This study investigates phytomer growth and development in Cleistogenes squarrosa, a predominant C4 grass in the Eurasian steppe, grown at low (0.63 kPa) or high (1.58 kPa) VPD with low or high nitrogen supply in controlled environments. Elongation of phytomers on marked tillers was measured daily for 13 days. Then lengths of immature and mature phytomer components (blade, sheath and internode) of all phytomers were measured following dissection. Nitrogen nutrition and VPD had no effects on coordination of growth within and between phytomers: phytomer tips emerged when phytomers reached 26 % of their final length, coincident with the acceleration phase of its elongation; blade elongation stopped when phytomers reached ∼75 % of their final length and elongation of the preceding phytomer was confined to the internode. The relationship between fraction of final phytomer length and days after tip emergence for all treatments was well described by a sigmoidal function: y = 1/{1 + exp[(1.82 - x)/1.81]}. C. squarrosa exhibited little morphological plasticity at phytomer-level in response to nitrogen supply and VPD, but a clear increase in tillering under high N supply. Also, the invariant coordination of elongation within and between phytomers was a stable developmental feature, thus the quantitative coordination rules are applicable for predicting morphological development of C. squarrosa under contrasting levels of nitrogen nutrition or VPD.
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Affiliation(s)
- Fang Yang
- Lehrstuhl für Grünlandlehre, Department für Pflanzenwissenschaften, Technische Universität München, Alte Akademie 12, D-85354 Freising, Germany
| | - Xiao Ying Gong
- Lehrstuhl für Grünlandlehre, Department für Pflanzenwissenschaften, Technische Universität München, Alte Akademie 12, D-85354 Freising, Germany
| | - Hai Tao Liu
- Lehrstuhl für Grünlandlehre, Department für Pflanzenwissenschaften, Technische Universität München, Alte Akademie 12, D-85354 Freising, Germany
| | - Rudi Schäufele
- Lehrstuhl für Grünlandlehre, Department für Pflanzenwissenschaften, Technische Universität München, Alte Akademie 12, D-85354 Freising, Germany
| | - Hans Schnyder
- Lehrstuhl für Grünlandlehre, Department für Pflanzenwissenschaften, Technische Universität München, Alte Akademie 12, D-85354 Freising, Germany
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Zhang X, Marcucci F, Firestein S. High-throughput microarray detection of vomeronasal receptor gene expression in rodents. Front Neurosci 2010; 4:164. [PMID: 21267422 PMCID: PMC3024560 DOI: 10.3389/fnins.2010.00164] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 08/18/2010] [Indexed: 11/13/2022] Open
Abstract
We performed comprehensive data mining to explore the vomeronasal receptor (V1R and V2R) repertoires in mouse and rat using the mm5 and rn3 genome, respectively. This bioinformatic analysis was followed by investigation of gene expression using a custom designed high-density oligonucleotide array containing all of these receptors and other selected genes of interest. This array enabled us to detect the specific expression of V1R and V2Rs which were previously identified solely based on computational prediction from gene sequence data, thereby establishing that these genes are indeed part of the vomeronasal system, especially the V2Rs. One hundred sixty-eight V1Rs and 98 V2Rs were detected to be highly enriched in mouse vomeronasal organ (VNO), and 108 V1Rs and 87 V2Rs in rat VNO. We monitored the expression profile of mouse VR genes in other non-VNO tissues with the result that some VR genes were re-designated as VR-like genes based on their non-olfactory expression pattern. Temporal expression profiles for mouse VR genes were characterized and their patterns were classified, revealing the developmental dynamics of these so-called pheromone receptors. We found numerous patterns of temporal expression which indicate possible behavior-related functions. The uneven composition of VR genes in certain patterns suggests a functional differentiation between the two types of VR genes. We found the coherence between VR genes and transcription factors in terms of their temporal expression patterns. In situ hybridization experiments were performed to evaluate the cell number change over time for selected receptor genes.
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Affiliation(s)
- Xiaohong Zhang
- Department of Biological Science, Columbia University New York, NY, USA
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